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| Message Board |
| CASP16 registration and format testing | (2024-4-13) |
Dear CASPers,
CASP16 registration is in full swing, with 83 groups already registered. The first CASP16 target will be released on Wednesday, May 1 at 9 am Pacific Time.
We will start a 'dry run' on checking format compliance and server connectivity on Tuesday, April 16. If you plan to enroll a server in CASP16, please do so as soon as possible so that we can test your server in the dry run and ensure flawless data transfer during the CASP16 prediction season. If you registered a human-expert group, you could also test the format of your model during the dry run by submitting a test prediction when the appropriate server test target is released.
The dry run will be conducted in four stages.
In the first stage (Tuesday-Thursday), we will test servers registered for protein and RNA tertiary structure prediction. We will release two test targets from the previous CASP - T1104 (protein) and R1117 (RNA) - and send their sequences to the registered servers. We expect the servers to return predictions in the requested TS format (https://predictioncenter.org/casp16/index.cgi?page=format#TS). Please check the Server Queries link from the main CASP16 web page (which will be available on Tuesday) to see the status of queries to your server. In case you notice any problems, please check your registration settings and contact us if in doubt. If you do not see your prediction(s) as accepted in our server status page (link Server Prediction Status) or through the Model Viewer /My CASP16 Profile pages, then either your prediction did not reach us, or was rejected due to an unregistered submission email or format issues.
On Thursday, we will start the second stage with testing automated predictors of protein and RNA oligomers. We will send you a query for a protein homodimer (T1124), protein heterodimer (H1106), and an RNA homodimer (R1107).
We will continue the dry run on Monday, April 22, with testing EMA servers on the released oligomeric targets.
And finally, starting Wednesday, April 24 we will be testing format for RNA oligomers (R1107) and protein-RNA(DNA) complexes (M1189). We would assume that your server can do RNA oligomers if it is registered for RNA prediction, and can do protein-RNA modeling if it is registered for both categories. Please write to us if this is not the case.
There will be no server prediction for ligand and ensembles targets.
CASP organizers
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| CASP16 - registration opens | (2024-4-1) |
Dear CASPers,
The CASP16 is upon us! This year, we celebrate the 30th anniversary of CASP experiments, and it promises to be an exciting milestone. Whether you’re a seasoned participant or a newbie, it’s time to showcase the strength of your methods in this upcoming round.
We have opened registration for the new prediction season at https://predictioncenter.org/casp16/registration.cgi.
Please register and stay tuned for more information on preparation and progress as we gear up for CASP16!
CASP16 organizers:
John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Maya Topf
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| CASP Special Interest Group on Modeling Ensembles and Alternative Conformations of Proteins | (2024-3-28) |
The next CASP SIG on Modeling Ensembles and Alternative Conformations of Proteins will be held via Zoom on Wednesday April 3, 2024 at 11:00 am EST.
This meeting with feature presentation by Bowen Jing from the groups of Bonnie Berger and Tommi Jaakkola at MIT, titled "AlphaFold Meets Flow Matching for Generating Protein Ensembles"
Zoom Link: https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
See also:
https://arxiv.org/abs/2402.04845
https://www.youtube.com/watch?v=yDDXF6XJZck
Agenda
Intro to CASP CE SIG – GT Montelione 5 min
“AlphaFold Meets Flow Matching for Generating Protein Ensembles” – Bowen Jing 35 min
Planning for CASP15 Multiple Conformations Experiment 20 min
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| Call for targets for the 2024 CASP modeling experiment | (2024-3-16) |
CASP (Critical Assessment of Structure Prediction) experiments are held every two years. Recent rounds have seen dramatic increases in modeling accuracy, resulting from the introduction of deep learning methods: In 2018, for the first time, the folds of most proteins were correctly computed [1]; in 2020, the accuracy of many computed protein structures rivaled that of the corresponding experimental ones [2]; in 2022, there was an enormous increase in the accuracy of protein complexes [3].
We have seen the beginning of what deep learning methods may achieve in structural biology. In addition to further increases in the accuracy of protein complexes, methods are being developed for RNA structures, organic ligand-protein complexes, and for moving beyond single macromolecular structures to compute conformational ensembles. Accurate computational methods together with experimental data also offer the prospect of probing previously inaccessible biological systems. CASP has expanded its scope to provide critical assessment in all these areas.
CASP is only possible with the generous participation of the experimental structural biology community in providing suitable targets: A total of over 1100 targets have been obtained over the previous CASP rounds. We are now requesting targets for the 2024 CASP16 experiment. We need challenge targets in the following areas:
Single protein structures: The 2020 and 2022 CASPs showed that, so far, Alphafold2 and methods built around it are by far the most accurate [4]. But there are limitations, particularly for some proteins where only a shallow sequence alignment is available and for very large proteins (more than 1000 amino acids). The best results also require substantial amounts of computing resources, well beyond that of the AlphaFold2 default settings. Many new methods are continuing to appear and these may remove some of the remaining difficulties. All types of protein targets are needed, but especially those with shallow sequence alignments, without structural templates, and large proteins.
Protein complexes: In the 2022 CASP15, advanced deep learning methods were applied to protein complexes for the first time [5]. The result was a huge improvement in accuracy compared with classical docking approaches. But overall, the results are still not at the level achieved for single proteins. So, in CASP16 we need all sorts of targets in this area so as to determine progress since then. We particularly need complexes where there is no evolutionary information across the protein-protein interfaces, for example, antibody-antigen complexes. (This CASP category is conducted in close collaboration with our colleagues at CAPRI - Critical Assessment of protein interactions [6]).
Nucleic acid structures and complexes: In recognition of the major role nucleic acid structures and complexes play in biology, CASP now includes this class of target. A number of papers claiming successful RNA structure computation using deep learning methods have been published, but those participating in the 2022 CASP RNA category performed less well than classical approaches, and no methods were able to effectively address the two RNA protein-complexes included [7]. CASP needs a wide variety of RNA, DNA, and complexes as targets to see if this situation has changed. (This CASP category is conducted in close collaboration with RNApuzzles [8]).
Organic ligand-protein complexes: This area is of major importance for computer-aided drug discovery. Earlier, there have been community experiments to assess the accuracy of methods, particularly SAMPL, CSAR, D3R, and a new one, CACHE, has recently started (cache-challenge.org). These challenges have drawn strong international participation from researchers in both academia and industry. Here too, a number of promising deep learning papers have appeared, but in the 2022 CASP15 pilot, classical methods were still superior [9]. So, we need appropriate targets to see if progress has been made since. Ideally, these should be sets of three-dimensional protein-ligand complexes from drug discovery projects, but single targets would also be appreciated. Additionally, where available, we will assess non-structural quantities such as affinities or affinity rankings and other properties of pharmaceutical interest when these are available (small molecule pKs, and DMPK related properties).
Ensembles of macromolecule conformations: It is now widely recognized that proteins and nucleic acids often adopt multiple conformations that can underpin their functions. In these cases, considering only a single protein or RNA conformation may be a significant oversimplification. The 2022 CASP15 included a pilot experiment to assess methods for computing multiple conformations, with encouraging results [10], but with limitations imposed by the available experimental data. For 2024, we seek not only cases of multiple experimental three-dimensional structures for the same macromolecule but also other types of data that might be used for assessment of computed conformation ensembles such as cryoEM, NMR, X-ray crystallography, SAXS, and/or cross-link data.
Integrative modeling: The more powerful computational methods open up new possibilities for combination with sparse or low-resolution experimental data to investigate previously inaccessible biological structures and machines. CASP is interested in exploring these possibilities and so requests experimentally difficult targets where structure has nevertheless been obtained. In appropriate cases, we expect to be able to collaborate with other experimental groups to provide appropriate data from NMR, cross-linking or SAXS.
There are three avenues to contribute a target to CASP:
1. (preferrable) Submit directly to CASP through our web-interface https://predictioncenter.org/casp16/targets_submission_form.cgi (requires a quick registration at https://predictioncenter.org/login.cgi if you do not have an account with us).
2. Email to targets@predictioncenter.org with your target suggestions or to discuss any questions.
3. Submit your structure to the PDB (on-hold) and designate it as a CASP target through PDB’s submission interface.
The timeline for the 2024 CASP requires that targets are submitted starting now and until July 1. We would like to hear from you as soon as possible if you may have something suitable or have suggestions about other target sources. In order to maintain rigor, the experimental data for a target must not be publicly available until after computed structures have been collected. For assessment, CASP requires the experimental data by August 15, but the data can remain confidential after that. Target providers are invited to contribute to papers [11-15] for a special CASP issue of the journal Proteins.
1. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins 2019;87(12):1011-1020.
2. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIV. Proteins 2021;89(12):1607-1617.
3. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XV. Proteins 2023;91(12):1539-1549.
4. Simpkin AJ, Mesdaghi S, Sanchez Rodriguez F, Elliott L, Murphy DL, Kryshtafovych A, Keegan RM, Rigden DJ. Tertiary structure assessment at CASP15. Proteins 2023;91(12):1616-1635.
5. Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Proteins 2023;91(12):1636-1657.
6. Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin A, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023;91(12):1658-1683.
7. Das R, Kretsch RC, Simpkin AJ, Mulvaney T, Pham P, Rangan R, Bu F, Keegan RM, Topf M, Rigden DJ, Miao Z, Westhof E. Assessment of three-dimensional RNA structure prediction in CASP15. Proteins 2023;91(12):1747-1770.
8. Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res 2020;48(2):576-588.
9. Robin X, Studer G, Durairaj J, Eberhardt J, Schwede T, Walters WP. Assessment of protein-ligand complexes in CASP15. Proteins 2023;91(12):1811-1821.
10. Kryshtafovych A, Montelione GT, Rigden DJ, Mesdaghi S, Karaca E, Moult J. Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. Proteins 2023;91(12):1903-1911.
11. Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins 2023;91(12):1600-1615.
12. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markusson S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Jr., Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023;91(12):1571-1599.
13. Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Bottcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021;89(12):1647-1672.
14. Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Jr., Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019;87(12):1037-1057.
15. Kryshtafovych A, Albrecht R, Basle A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes C, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2018;86 Suppl 1(Suppl 1):27-50.
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| CASP Special Interest Group on Modeling Ensembles and Alternative Conformations of Proteins | (2024-3-1) |
The next CASP SIG on Modeling Ensembles and Alternative Conformations of Proteins will be held via Zoom on Wednesday March 6, 2024 at 11:00 am EST.
This meeting with feature presentation by Bruce Donald, PhD and Terry Oas, PhD (Duke University, Departments of Biochemistry and Computer Science)
Zoom Link: https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
Agenda
Intro to CASP CE SIG – GT Montelione 5 min
“Structure of a Two Domain Protein with a Flexible Linker: A Continuous Distribution of Interdomain Orientations Derived from NMR Residual Dipolar Couplings” – B Donald & T Oas 35 min
Planning for CASP15 Multiple Conformations Experiment 20 min
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| Special Interest Group on Modeling Ensembles and Alternative Conformations of Proteins - Wednesday Feb 7 at 11:00 am EST | (2024-1-30) |
Join us for the next CASP SIG on Modeling Ensembles and Alternative Conformations of Proteins will be held by Zoom on Wednesday February 7, 2024 at 11:00am EST. Presentation by Susan Tsutakawa. Ph.D. and John Tainer, Ph.D. Lawrence Berkeley National Laboratory and MD Anderson Cancer Center, University of Texas - Houston
Zoom Link:
https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
Agenda
GT Montelione. Organizing CASP16 experiment on conformational ensembles - 10 min
S Tsutakawa - “A glimpse at solution state ensembles: From the CASP-Small Angle X-ray Scattering (SAXS) perspective” - 30 min
Open discussion - 20 min
Vision Statement:
Recognizing that biomolecules do not have static structures, but rather adopt a distribution of conformational states. The CASP- SIG aims to evaluate if a critical assessment of predictions of conformational ensembles or multiple conformational states of biomolecules is feasible. The SIG will consider developments in the fields of structural and computational biology that are anticipated in the next 2-5 years and define protocols for assessing the accuracy of ensemble model predictions.
Past presentations are available on YouTube https://youtube.com/@MontelioneLab?si=6yJzKHHBTb_ICI3X
For future speaker and topic/ presentation suggestions, to access video recordings and slide presentations, or to be added on the group mailing list - Contact montelionelab@rpi.edu
Connect on Linkedin: https://www.linkedin.com/groups/12747534/
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| January 3 - CASP Special Interest Group on Modeling Ensembles and Alternative Conformations of Proteins | (2024-1-1) |
Happy New Year everyone!
The next CASP SIG on Modeling Ensembles and Alternative Conformations of Proteins will be held by Zoom on Wednesday January 3, 2024 at 11:00am EST. It will feature discussions on representing alternative conformational states by Gaetano T. Montelione, PhD (Rensselaer Polytechnic Institute) and James Fraser, PhD and Stephanie Wankowicz, PhD (University of California San Francisco) .
Zoom Link:
https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
Agenda
Intro to CASP CE SIG - GT Montelione 5 min
Representing structures of the multiple conformational states of proteins
https://www.sciencedirect.com/science/article/pii/S0959440X2300177X
GT Montelione 20 min
Comprehensive encoding of conformational and compositional protein structural ensembles through mmCIF data structure
(https://chemrxiv.org/engage/chemrxiv/article-details/655cd6bb2c3c11ed71d888a9).
J Fraser and S Wankowicz 20 min
Open Questions and Discussion 15 min
Vision Statement:
Recognizing that biomolecules do not have static structures, but rather adopt a distribution of conformational states. The CASP- SIG aims to evaluate if a critical assessment of predictions of conformational ensembles or multiple conformational states of biomolecules is feasible. The SIG will consider developments in the fields of structural and computational biology that are anticipated in the next 2-5 years and define protocols for assessing the accuracy of ensemble model predictions.
Past presentations are available on YouTube https://youtube.com/@MontelioneLab?si=6yJzKHHBTb_ICI3X
For future speaker and topic/ presentation suggestions, to access video recordings and slide presentations, or to be added on the group mailing list - Contact montelionelab@rpi.edu
Connect on Linkedin: https://www.linkedin.com/groups/12747534/
Gaetano Montelione,
for the SIG organizers
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| CAPRI meeting in Grenoble, Feb 12-16, 2024 | (2023-12-20) |
On the behalf of the CAPRI meeting organizers:
Dear colleagues,
We would like to announce a joint event combining a workshop on algorithms for integrative structural biology as well as a CAPRI (protein interactions) meeting. The goal will be to present the current algorithmic state of the art in the modelling field and also to discuss the needs and unsolved cases with the experimentalists. We expect some of the talks to be experimental – these will be ‘negative cases’, unsolved structures, and future challenges.
The workshop will take place at the EPN site, Grenoble (ESRF/ILL/EMBL/IBS) on February 12-16 2024. The scientific committee is composed of Martin Blackledge (IBS Grenoble), Alexandre Bonvin (Utrecht University), Frederic Cazals (Inria Sophia Antipolis), Sergei Grudinin (CNRS Grenoble), Anne Martel (ILL), Sylvain Prevost (ILL), Guy Schoehn (IBS Grenoble), Martin Weik (IBS Grenoble), and Shoshana Wodak (VIB Brussels).
We encourage you to register and submit a talk abstract on the current bottlenecks in your research field and possibly about the integrative methods and their computational aspects. We, of course, expect deep-learning related talks, but we would also like to encourage more classical methods and experimental work. And we would like to avoid, if possible, AF2-based talks, as there are other workshops organized around AF2.
The workshop website : https://workshops.ill.fr/event/392/ (with a shortcut https://workshops.ill.fr/e/icbm2024) and its email : icbm2024@ill.fr
The registration deadline is Jan 15, 2024. Please register in advance so we can estimate the number of talks.
Registration fees are 200 € for both meetings, or 90 € for the ICB workshop alone and 130 € for the CAPRI meeting alone, and include:
• Lunches at the onsite restaurant;
• Coffee breaks;
• Wine & Cheese buffet on Tuesday evening for participants to the ICB workshop;
• Dinner on Thursday for the participants to the CAPRI meeting and tram tickets to reach the restaurant.
Participants can book a room at the EPN-campus Guest-House or at the Marie-Curie Residence, directly from the Registration form (Registration tab). The rate for a single room is 60 EUR per night (breakfast included).
Participants willing to book themselves a hotel are recommended to select those near the Tram B public transport, as it reaches (and stops at) the EPN campus where the meeting is organized ("Oxford '' tram stop). For example, Hôtel de l'Europe or Le Grand Hôtel de Grenoble (Best Western), Novotel Grenoble Centre or RockyPop Grenoble. If you plan a longer stay, you can check out ResidHome.
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| Wed, December 6 - CASP SIG on Modeling Ensembles - Lauren Porter (NIH) | (2023-12-1) |
The next meeting of CASP SIG on Modeling Ensembles and Alternative Conformations
will be held by zoom on Wednesday Dec 6, 2023 at 11:00 AM EDT (New York time).
Agenda for Weds Dec 6th:
Short Intro to CASP16 Multiple Conformation Experiment
Speaker: Lauren Porter, NIH/NLM/NCBI. "Evolutionary selection of proteins with two folds"
General Discussion: Multiple conformational states in CASP16
Zoom Link
https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
Gaetano T. Montelione
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| CASP15 special issue of PROTEINS published | (2023-11-24) |
Dear CASPers,
The CASP15 special issue of PROTEINS has been published as a December 2023 issue of the journal. All papers are open or free access, so everyone can access them without charge:
https://onlinelibrary.wiley.com/toc/10970134/2023/91/12
We want to thank all the contributors to the issue and remind everyone that CASP16 is only half a year away. But for the moment - Happy Thanksgiving and best wishes for the upcoming winter holidays,
CASP organizers
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| OpenChallenges.io | (2023-11-7) |
On behalf of Drew Duglan, Principal, Communications and Marketing, Sage Bionetworks:
OpenChallenges.io just went live officially!
Please check
Press release: https://sagebionetworks.org/in-the-news/open-challenges/
The fact sheet/media resources: https://docs.google.com/document/d/11KUGEAB-5gf0ZvGMH5mbRzWjNDu4VzGp609pUmcFtjw/edit?usp=sharing
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| CASP SIG on Modeling Ensembles and Alternative Conformations - Wah Chiu and Martin Blackledge - Wednesday October 4, 2023 | (2023-9-28) |
The next meeting of CASP SIG on Modeling Ensembles and Alternative Conformations will be held by zoom on Wednesday October 4, 2023 at 11:00 AM EDT (New York time).
We will have 2 presentations, about 30 min each including questions.
Then - for people available - we will continue to discuss for ~ 30 how to develop a CASP SIG on Multiple Conformations for 2024.
Agenda for Weds October 4th
Wah Chiu, Stanford University, USA “Resolving proteins in multiple conformations with cryoEM”
Martin Blackledge, Institute of Structural Biology, Grenoble, FRANCE. "NMR provides unique Insight into the functional dynamics of intrinsically disordered proteins”
General Discussion - Multiple conformational states in CASP
each talk should be ~ 20 min with 10 min for questions
zoom link: https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
Future Presentations (tentative titles)
Weds Nov 1
Jens Meiler. Vanderbilt University, USA & University Leipzig, GERMANY. "Targeting GPCR conformations with ultra-large library screening for hit discovery"
Vision Statement:
Recognizing that biomolecules do not have static structures, but rather adopt a distribution of conformational states. The CASP- SIG aims to evaluate if a critical assessment of predictions of conformational ensembles or multiple conformational states of biomolecules is feasible. The SIG will consider developments in the fields of structural and computational biology that are anticipated in the next 2-5 years, and define protocols for assessing the accuracy of ensemble model predictions.
We are looking forward to further development of this special interest group and are encouraging members of the group to share ideas, suggest discussion topics, network and facilitate collaboration within the field. See you all October 4th.
For future speaker and topic suggestions, to access video recordings and slide presentations, or to be added on the group mailing list - Contact montelionelab@rpi.edu
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| September 6 - CASP SIG on Modeling Ensembles and Alternative Conformations | (2023-8-28) |
The next meeting of CASP SIG on Modeling Ensembles and Alternative Conformations will be held by zoom on Wednesday September 6th, 2023 at 11:00 AM EDT (New York time).
Agenda for Weds September 6th
Björn Wallner, Linköping University, SWEDEN. "Predicting multiple conformations of proteins using aggressive sampling in AlphaFold”
Wim Vranken, Vrije Universiteit Brussels, BELGIUM. "Defining and predicting conformational states and their variability”
zoom link: https://lnkd.in/dYC3CWSE
Future Presentations (tentative titles)
Weds Oct 4.
Wah Chiu, Stanford University, USA “Resolving proteins in multiple conformations with cryoEM”
Martin Blackledge, Institute of Structural Biology, Grenoble, FRANCE. "NMR provides unique Insight into the functional dynamics of intrinsically disordered proteins”
Weds Nov 1
Jens Meiler. Vanderbilt University, USA & University Leipzig, GERMANY. "Targeting GPCR conformations with ultra-large library screening for hit discovery"
Vision Statement: Recognizing that biomolecules do not have static structures, but rather adopt a distribution of conformational states. The CASP- SIG aims to evaluate if a critical assessment of predictions of conformational ensembles or multiple conformational states of biomolecules is feasible. The SIG will consider developments in the fields of structural and computational biology that are anticipated in the next 2-5 years, and define protocols for assessing the accuracy of ensemble model predictions.
We are looking forward to further development of this special interest group and are encouraging members of the group to share ideas, suggest discussion topics, network and facilitate collaboration within the field, see you all September 6th.
For future speaker and topic suggestions or to be added on the group mailing list - Contact montelionelab@rpi.edu
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| 2nd RNA SIG meeting - Tuesday, June 6, 8am PDT | (2023-6-5) |
Dear RNA enthusiasts!
Join us for our second RNA CASP SIG meeting with a presentation from Dr. Frank DiMaio:
Predicting protein/nucleic acid complexes with RoseTTAFoldNA
Tuesday, June 6 Pacific Time 8am / Eastern Time 11am / Central European Time: 5pm / China Standard Time: 11pm
Zoom link:
https://stanford.zoom.us/j/93445935624?pwd=K0VUWk0zaVNMZlU1U0xUMS8vSWUwZz09
If you have recommendations on topics of discussion or speakers, please feel free to email us as well. We aim to meet virtually monthly to discuss the state of and new developments in our community. https://groups.google.com/g/casp-rna-sig and click "Ask to join group"
Rachael Kretsch (Rhiju Das and Wah Chiu labs @Stanford)
Marcin Magnus (Elena Rivas lab @Harvard)
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| The third meeting of the CASP SIG on Modeling Ensembles and Alternative Conformations | (2023-6-5) |
The third meeting of the CASP SIG on Modeling Ensembles and Alternative Conformations will be held on Wednesday June 7, 2023 at 11:00 am EDT (NY time)
These meetings are held by zoom on first Wednesday of each month, at 11:00 AM EDT (New York time). Meetings are also scheduled on Jul 5 and Sept 6.
Vision Statement: Recognizing that biomolecules do not have static structures, but rather adopt a distribution of conformational states, this CASP SIG aims to evaluate if a critical assessment of predictions of conformational ensembles or multiple conformational states of biomolecules is feasible. The SIG will consider developments in the fields of structural and computational biology that are anticipated in the next 2-5 years, and define protocols for assessing the accuracy of ensemble model predictions.
Videos and Slides from our previous meetings are available: https://lnkd.in/dNvBNx4T
Linked in group: https://lnkd.in/eCSK-FBZ
Agenda for Jun 7 at 11:00 am EDT
Hannah Wayment-Steele, Brandeis University, USA (20 min)
Prediction of multiple conformational states of proteins by combining sequence clustering with AlphaFold2
Rhiju Das, Stanford University, USA (20 min)
Observing multiple conformational states of RNA by cryoEM
Questions and Open Discussion (20 min)
Can we implement a CASP experiment on predicting multiple conformational states of proteins? Role of cryoEM?
Join Zoom Meeting
https://lnkd.in/dYC3CWSE
Meeting ID: 816 6397 5964
Passcode: 182245
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| First RNA SIG meeting - Tuesday, May 23, 8am PDT | (2023-5-17) |
Dear RNA structure enthusiasts,
We would like to present you with our first RNA CASP Special Interest Group (SIG) speaker, Dr. Yu Li.
“RNA structure prediction with deep learning”
Tuesday, May 23, Pacific Time 8am / Eastern Time 11am / Central European Time: 5pm / China Standard Time: 11pm
Following the presentation and Q&A, we will engage in a discussion regarding the organization of our SIG for future meetings. If you have recommendations on topics of discussion or speakers, please feel free to email us as well.
See you!
Rachael Kretsch (Rhiju Das and Wah Chiu labs @Stanford)
Marcin Magnus (Elena Rivas lab @Harvard)
Zoom link: https://stanford.zoom.us/j/93445935624?pwd=K0VUWk0zaVNMZlU1U0xUMS8vSWUwZz09
TALK ABSTRACT
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we proposed an RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discovered that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Building upon RNA-FM, we proposed a deep learning method, RhoFold, to predict the RNA 3D structure in an end-to-end fashion. We evaluated RhoFold using all the publicly available 3D structure data, on which it performs impressively. We will also discuss the limitations and potential improvement of RhoFold.
SPEAKER BIO
Yu Li joined the Department of Computer Science & Engineering at the Chinese University of Hong Kong in December 2020 as an assistant professor, leading the Artificial Intelligence in Healthcare (AIH) group. He is also the Visiting Assistant Professor at MIT/Harvard, working with Prof. James Collins. He works at the intersection between machine learning, healthcare and bioinformatics, developing new machine learning methods to resolve the computational problems in biology and healthcare. He has published over 50 papers in top venues, such as Nature Communications, PNAS, and Nature Computational Science. In 2022, he was selected to the Forbes 30 Under 30 Asia list, Healthcare & Science. He obtained his Ph.D. in computer science from KAUST in Saudi Arabia in 2020, after which he was nominated KAUST Alumni Change Makers Awards in 2022. Before that, he got the Bachelor degree in Biosciences from University of Science and Technology of China (USTC).
CASP RNA SIG:
Welcome to the Special Interest Group (SIG) focused different aspects of nucleic acid 3D structure prediction, including but not limited to obtaining experimental data, building train and test sets, RNA alignments, ligand interactions, ensembles etc. We aim to meet virtually monthly to discuss the state of and new developments in our community. We hope also to foster an active Google group for email correspondence.
How to use google groups:
To send a message to the group: simply send an email to casp-rna-sig@googlegroups.com.
For a new member to request: Go to https://groups.google.com/g/casp-rna-sig and click "Ask to join group"
To view past messages: Go to https://groups.google.com/g/casp-rna-sig (must be a member of group).
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| CASP SIG meeting on Modeling Ensembles and Alternative Conformations - May 3 | (2023-4-28) |
The second meeting of the CASP SIG on Modeling Ensembles and Alternative Conformations will be held on Wednesday May 3, 2023 at 11:00 am EDT (NY time)
The meetings are held by zoom on first Wednesday of each month, at 11:00 AM EDT (New York time). Meetings are also scheduled on Jun 7 and Jul 5.
Vision Statement: Recognizing that biomolecules do not have static structures, but rather adopt a distribution of conformational states, the CASP SIG aims to evaluate if a critical assessment of predictions of conformational ensembles or multiple conformational states of biomolecules is feasible. The SIG will consider developments in the fields of structural and computational biology that are anticipated in the next 2-5 years, and define protocols for assessing the accuracy of ensemble model predictions.
Videos and Slides from our meeting March 1, 2023 are available: https://rpi.box.com/s/qltlfgndkqq16j985d3pl6z1gargl5gi
Agenda for May 3 at 11:00 am EDT
Shoshana J Wodak, VIB-VUB Center for Structural Biology, Brussels (20 min)
Charting and characterizing the conformational landscape of native proteins:
an Implementation Study of the 3DBioInfo Elixir Community.
Michael Feig, Michigan State University. (20 min)
Modeling multiple conformational states of proteins
Questions and Open Discussion (20 min)
Can we implement a CASP experiment on predicting multiple conformational states of proteins?
Gaetano Montelione is inviting you to a scheduled Zoom meeting.
Topic: CASP SIG on Alternative Conformations and Ensembles
Time: May 3, 2023 11:00 AM Eastern Time (US and Canada)
Every month on the First Wed, 3 occurrence(s)
May 3, 2023 11:00 AM
Jun 7, 2023 11:00 AM
Jul 5, 2023 11:00 AM
Please download and import the following iCalendar (.ics) files to your calendar system.
Monthly: https://us02web.zoom.us/meeting/tZUrceqhqT4jHNCi1l1hdLvw21_B1fBq6fwY/ics?icsToken=98tyKuGpqD0pE9OQuR-DRpwcBI_ob_PwtiVEgo1-lU7pUihXThXhZLN9EON5MsmG
Join Zoom Meeting
https://us02web.zoom.us/j/81663975964?pwd=Rkt4NjhGQUYra3ZGTEJxR2szdjRwZz09
Meeting ID: 816 6397 5964
Passcode: 182245
If you would like to be added to the mailing list for this SIG, please email: montelionelab@rpi.edu
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| First seminar of the CASP Special Interest Group on Ensembles of Alternative Conformations | (2023-2-28) |
We have organized a CASP Special Interest Group on Ensembles of Alternative Conformations to provide discussions of methods for modeling alternative conformations of proteins and nucleic acids, and for assessing these methods in a CASP-like experiment.
In this first meeting Prof John Moult will describe what was learned in the CASP15 pilot experiment on target types and the prediction for alternative conformations.
A zoom link for this meeting is provided below.
Agenda
10 min - overview of goals of the SIG on Ensembles of Alternative Conformations
30 min - Alternative Conformations in CASP15 - John Moult, Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland.
20 min - general discussion of the challenge to develop a CASP16 experiment on alternative conformations
We have also established a LinkedIn Group to share information on this topic; pls join this group if you have interests in this topic.
https://www.linkedin.com/groups/12747534/
Topic: CASP SIG on Ensembles of Alternative Conformations
Time: Mar 1, 2023 11:00 AM Eastern Time (US and Canada)
Join Zoom Meeting
https://us02web.zoom.us/j/88068029210?pwd=bXNobEF6ZHg1b1ZkdFQ1SWlVa2ZQQT09
Meeting ID: 880 6802 9210
Passcode: 443092
Gaetano Montelione
Damiano Piovesan
Silvio Tosatto
Chin-Hsien (Emily) Tai
Wim Vranken
Shosana Wodak
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| CASP Special Interest Group on Ensembles of Alternative Conformations | (2023-2-9) |
We have organized a CASP Special Interest Group on Ensembles of Alternative Conformations
to provide discussions of methods for modeling alternative conformations of proteins and
nucleic acids, and for assessing these methods in a CASP-like experiment.
The first meeting of this CASP SIG will be held on Mar 1, 2023 at 11:00 am - 12:00 noon EST.
A zoom link for this meeting is provided below.
In this first meeting Prof John Moult will summarize the results of the Alternative Conformations experiment
in CASP15.
Agenda
10 min - overview of goals of the SIG on Ensembles of Alternative Conformations
30 min - Alternative Conformations in CASP15 - John Moult, Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland.
20 min - general discussion of the challenge to develop a CASP16 experiment on alternative conformations
We have also established a LinkedIn Group to share information on this topic; pls join this group if you have interests in this topic.
https://www.linkedin.com/groups/12747534/
Topic: CASP SIG on Ensembles of Alternative Conformations
Time: Mar 1, 2023 11:00 AM Eastern Time (US and Canada)
Join Zoom Meeting
https://us02web.zoom.us/j/88068029210?pwd=bXNobEF6ZHg1b1ZkdFQ1SWlVa2ZQQT09
Meeting ID: 880 6802 9210
Passcode: 443092
Gaetano Montelione
Damiano Piovesan
Silvio Tosatto
Chin-Hsien (Emily) Tai
Wim Vranken
Shoshana Wodak
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| Reposting: Postdoctoral position at the Protein Structure Prediction Center, UC Davis | (2023-1-10) |
We are still looking for a postdoc to help with CASP-related issues - see the posting below.
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A one-year position focused on large scale analysis of model accuracy with respect to applications in structural biology and biology in general.
The UC Davis Protein Structure Prediction Center provides the infrastructure to the Critical Assessment of protein Structure Prediction program (CASP), dedicated to cutting-edge science in modeling of protein structure. It brings together approximately 100 research groups from more than 20 countries world-wide.
Desirable skills:
1. In depth knowledge of protein structure
2. Fluency in programming (Perl, PostgreSQL, Python, R and C)
3. Familiarity with Linux
4. Ability to write and run scripts processing data
5. Basic knowledge of computer system administration, including multi-processor clusters
6. Knowledge of cgi scripting, web design, and online data visualization tools is also desirable
The position is available immediately. With inquiries, please contact Krzysztof Fidelis (kfidelis@ucdavis.edu).
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| CASP Special Interest groups | (2023-1-5) |
One outcome of the CASP15 conference was a decision to create CASP special interest groups (SIGs) with the goal of increasing communication and discussion of new CASP-related developments. This message provides an update on how SIG plans are progressing and invites participation. There are currently four initiatives:
1. AI methods in structural biology led by Arne Elofsson: This group plans to meet monthly (2nd Wednesday. 17:00 Sweden time), and will also cover a broader range of CASP topics. Please join the mailing list if you are interested: https://groups.google.com/g/casp-zoom/members
More information at: https://casp.bioinfo.se/
2. Multiple Conformations and Ensembles led by Guy Montelione: Those interested are invited to join the Linkedin group at
https://www.linkedin.com/groups/12747534/
3. RNA structure: Those interested should contact Rachael Kretsch at rkretsch@stanford.edu. If you are interested in playing a larger role in organizing the RNA SIG please mention that in your email.
4. Macromolecular complexes: Roland Dunbrack is exploring ways of collaboratively building models of large molecular machines of major biological interest. If you would like to be involved in this please, contact him at Roland.Dunbrack@fccc.edu
It would be great if there were also an active SIG on Ligand/protein complexes. If you are interested in this please get in touch.
CASP also has a DISCORD with channels for these and other topics: https://discord.com/invite/gQgSQkCzH7
CASP organizers
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| AI/mathematical modeling - Structural biology meeting, March 2023, South of France | (2023-1-3) |
Dear Colleague,
I would like to bring your attention to the next DaiSB (Directions in AI for Structural Biology) conference that will take place March 20-24, 2023, at the CIRM (Centre International de Rencontres Mathématiques) Marseille, France: Interplay between AI and mathematical modelling in the post-structural genomics era.
We aim to bring together experts from the machine learning, mathematical modelling and computational biology communities. The conference will highlight recent developments at the interface of these areas, focusing on protein and nucleic acid sequences, structures and functions. We welcome contributions addressing relevant questions of methodology, applications, and synergies with experimental biology. We are also enthusiastic about receiving contributions not directly linked to proteins and nucleic acids (e.g., relevant to 3D geometry and equivariance, language modelling, interpretability and explainability).
We will cover three main directions:
- the interpretation of the representations (or embeddings) learnt by deep learning techniques
- the rational design of deep neural network architectures and building of input data representations.
- the efficient analysis and evaluation of the data generated by predictive deep learning approaches.
If you are interested, please pre-register at:
https://conferences.cirm-math.fr/2767.html
Extended deadline: January 20, 2023.
Detailed information about the previous edition can be found here: https://conferences.cirm-math.fr/2700.html
The meeting cost is $200 ($100 students, $1000 industry) plus accommodation charges (€105 per day, including all meals). Accompanying persons are accepted. Payment details are communicated after pre-registration validation.
Do not hesitate to spread the word to colleagues who might be interested!
We hope to see you soon at CIRM!
Krzysztof,
on behalf of the organizing committee: Krzysztof Fidelis, Sergei Grudinin, and Elodie Laine.
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| Abstracts and CASP program are available online; conference registration is still open | (2022-11-28) |
Dear CASPers,
1. CASP15 abstracts and conference program are now available online from the http://predictioncenter.org/casp15 web page.
2. You still can register for the conference by following a link from the PredictionCenter website.
CASP organizers
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| In preparation for the CASP15 conference: visa, posters, gala dinner | (2022-11-28) |
Dear CASPers,
If you are participating in CASP15 in Antalya (Dec. 10-13, 2022), you should have received instructions on how to reserve your poster presentation space, select the Gala Dinner menu, and check on the Turkish visa requirements. Please check your mailboxes and register your selections before December 2.
Please let us know if you did not receive these instructions (but you are going to participate in the Antalya meeting).
CASP organizers
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| Postdoctoral position at the Protein Structure Prediction Center, UC Davis | (2022-11-2) |
A one-year position focused on large scale analysis of model accuracy with respect to applications in structural biology and biology in general.
The UC Davis Protein Structure Prediction Center provides the infrastructure to the Critical Assessment of protein Structure Prediction program (CASP), dedicated to cutting-edge science in modeling of protein structure. It brings together approximately 100 research groups from more than 20 countries world-wide.
Desirable skills:
1. In depth knowledge of protein structure
2. Fluency in programming (Perl, PostgreSQL, Python, R and C)
3. Familiarity with Linux
4. Ability to write and run scripts processing data
5. Basic knowledge of computer system administration, including multi-processor clusters
6. Knowledge of cgi scripting, web design, and online data visualization tools is also desirable
The position is available immediately. With inquiries, please contact Krzysztof Fidelis (kfidelis@ucdavis.edu).
PS. It is still possible to register for CASP15 conference in Antalya - see https://predictioncenter.org/casp15.
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| Deadline for Methods Abstract(s) - tomorrow | (2022-9-14) |
A reminder: If you have not done so - please submit your abstracts by tomorrow, September 15:
https://predictioncenter.org/casp15/abstracts.cgi
CASP organizers
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| Regular registration for the CASP15 Antalya meeting closes this Friday! | (2022-9-13) |
Please register now at
https://www.eventbrite.com/e/casp15-tickets-405898973757
for the Antalya conference (December 10-13, 2022).
After September 16 registration fees will go up substantially and participation will not be guaranteed.
The conference will include sessions on:
Predicting protein 3D structure – do the newer methods surpass AlphaFold2?
Predicting protein complexes – just how much difference does deep-learning make?
Predicting RNA 3D structure – does deep leaning work here?
Predicting ligand-protein complexes – contributing more to drug design?
Predicting accuracy for models of proteins and complexes – how reliable really?
Predicting ensembles – challenges and how they may be overcome.
SIG sessions exploring the way ahead.
Poster sessions and extensive opportunities for in-person discussion.
All this and more in beautiful Antalya.
CASP organizers
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| Register for the Antalya SIGs – fill out the Survey (deadline Wednesday, September 7, 2022) | (2022-9-5) |
Please let us know what you think about the SIGs:
https://forms.gle/xz5f9tgtk5bWc9j66
Register for the Antalya CASP15 meeting (the deadline is September 16, 2022) using the following link at the CASP15 web page:
https://www.predictioncenter.org/casp15
CASP organizers
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| Submit your Methods Abstract(s) by September 15. | (2022-8-31) |
Now, when the CASP15 prediction activity is over and the assessors started their work, it is time to submit write-ups of your CASP15 methods. We have opened a web page for collecting the abstracts (https://predictioncenter.org/casp15/abstracts.cgi). Please read the instructions carefully and address all the questions specified in the Abstract submission form. The submission deadline is September 15, 2022.
CASP organizers
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| SIGs at the CASP conference in Antalya (survey deadline is September 7, 2022) | (2022-8-31) |
We are looking at ways of productively expanding the scientific activities at the in-person December CASP conference. In addition to Keynotes, assessor and predictor talks, main session discussions and posters, we would like to include some special interest group sessions (SIGs). Possible topic areas that have been suggested are Deep learning methods for structure and function prediction; RNA structure modeling; Protein-protein, Protein-RNA, and Protein-ligand complexes; and Modeling protein ensembles. The idea is that there will be some pre-conference interactions between those interested in each topic via our DISCORD channel in order to prepare, and then one or more breakout sessions at the conference, hopefully setting the stage for ongoing interactions after that.
We would like to gauge interest and potential participation levels in different topics, as well as to prepare adequate facilities in Antalya. Please let us know if you would like to participate in these groups, indicating which of the proposed topics or an additional one you are interested in. Also please indicate whether you are willing to be a leader of a topic.
Please answer the Survey questions at:
https://forms.gle/xz5f9tgtk5bWc9j66
The CASP15 meeting registration is accessible by following the link from the CASP15 web page:
https://www.predictioncenter.org/casp15 .
The deadline for registering for the meeting is September 16, 2022.
CASP organizers
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| Registration for the CASP15 conference is now open! | (2022-8-22) |
The first stage of the CASP15 community experiment to determine and advance the state of the art in modeling of macromolecular structures is now complete. 53,000 predictions on about 100 prediction targets have been collected, covering single proteins and domains, protein complexes, RNA structures, and protein-ligand complexes, and some conformational ensembles. Assessment is just getting underway, but it’s already clear there are some pretty exciting results! There will be an in-person CASP15 in Antalya, Turkiye, December 10-13, 2022.
Both active participants in the experiment and anyone interested in recent advances in this field are invited to attend. Presentations are expected from independent assessors and from successful structure predictors. Discussions, poster presentations, and a job fair are also planned.
The challenges of organizing an in-person meeting in the post-pandemic environment are considerable, so we ask that you complete your registration promptly, within four weeks, with a closing date of September 16. After that the registration fees will go up significantly (see below) and participation cannot be guaranteed. We will try to keep the possibility of adjusting the arrival and departure dates, up to two additional nights before and after the conference, for a few weeks past the September 16 registration deadline.
Registration fees include accommodation and all meals at a comfortable 5-star conference venue. We are happy to say that total cost is a little less than the last in-person conference (CASP13).
Dates: December 10 (3:30PM) - 13 (12:00PM), 2022
Place: Akra Hotel and Conference Center, Antalya, Turkiye
Registration fee (single occupancy): $1,300 ($2,000 after September 16), additional hotel nights $127
Registration fee (shared room): $1,200 ($1,900 after September 16), additional hotel nights $94
In case of a cancellation, refunds will be issued until September 16, 2022. We cannot guarantee refunds past that date.
Please register at:
https://www.eventbrite.com/e/casp15-tickets-405898973757
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| End of CASP15 | (2022-8-19) |
That's it. CASP15 prediction season is over. It was yet another interesting and fruitful season. The tertiary structure prediction continues to be the most populous category with 135 groups participating. Preliminary evaluation of models shows some very interesting results. Assembly prediction was a blast with 86 groups participating and predicting 47 targets. RNA prediction and Ligand prediction were two new categories, and we are happy to see that CASP stirred significant interest in these prediction areas. Participation exceeded our most optimistic expectations with 42 groups taking on 12 targets in the RNA category, and 33 groups taking on 27 targets in the ligand category.
Now, as they say in the airplanes, sit back and relax while our computers work round the clock crunching numbers for more than 53000 collected models. Evaluation is in full swing now, and assessors already started analyzing the results.
CASP organizers
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| CASP15: last week of prediction; get ready for abstracts; conference registration starts soon | (2022-8-13) |
Only one week left to go in CASP15! In that week we will be collecting models on the remaining seven prediction targets.
After the prediction activity is over, we will start collecting methods descriptions for the CASP15 Abstract book. The abstracts will be collected from September 1 till September 15 and published electronically at the Prediction Center website. Detailed requirements for the preparation of abstracts will be published shortly, however you can start preparing your abstracts already now based on the templates from the previous CASPs. Those participating in CASP for the first time can check the CASP14 Abstract book at https://predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf.
We are in the last stages of arranging the CASP15 conference (planning it in-person) and are hoping to open the registration in the next couple of weeks.
CASP organizers
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| CASP15: July 30, end of target release | (2022-7-30) |
Yesterday we released the last prediction target in CASP15. All in all, we offered 127 targets in four prediction categories, including 94 targets for tertiary structure prediction, 47 targets for oligomeric prediction (more than 50% increase compared to CASP14), 12 targets for RNA prediction (including 2 RNA-protein complexes) and 23 targets for the ligand binding prediction.
In the next three weeks, we will continue collecting models for the already released targets, and also continue sending closed oligomeric targets for the estimation of model accuracy.
CASP organizers
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| CASP15: week 13 (July 25-31) | (2022-7-23) |
We are at the doorsteps of the last week of CASP15 target release. Six targets are lined up, one-two more are hopeful. As it stands now,
on Monday, we would have a decamer homomeric complex;
on Tuesday, we will release a ~1300 residue-long sequence;
on Wednesday, we would have a regular target, and additionally the first target from the series of three protein kinases with multiple conformations;
on Thursday and Friday, we would have the other two targets from the kinase series.
If additional targets become available, those will be added to the Thursday and/or Friday releases.
The kinase targets (T1195-97) were solved with an advanced NMR technique, and for each of them, two to three structural conformations are present. We encourage predictors to model the alternative conformations and submit them within the CASP allowance of 5 models per target.
This would wrap up CASP15 target release season.
CASP organizers
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| CASP15: weeks 12 and 13 (July 18-31) | (2022-7-16) |
The last two weeks of CASP15 target release season will be packed with interesting targets. We will see large assembly complexes, protein-ligand complexes, targets with alternative conformations, and even a protein-RNA complex!
The first week (July 18-24) will start with a large heteromeric complex. Since this complex is big, we will allow extra time for both server and human prediction.
Tuesday will be free for tertiary/assembly prediction, but not for the ligand prediction. We will have a protein-ligand complex, where the structure of protein is known. The challenge would be to predict binding site and pose of the ligand. Additional information will be provided with the target release.
Wednesday will feature two more protein-ligand complexes.
On Thursday, we will have two RNA-protein complexes. The complexes represent alternative conformations corresponding to different particles in the same cryo-EM data set. The complexes contain one RNA molecule and several (4 or 6) protein molecules. Four targets will be released: T1189/R1189 pair for the A1(RNA):B6(prot) complex, and T1190/R1190 pair for the A1(RNA):B4(prot) complex. Predictions for each pair should be submitted in the same frame of reference so that concatenation of corresponding models for, say, T1189 and R1189 will give a coordinate set for the full RNA-protein complex.
The week will end with a long single-sequence target of ~1800 res.
Detailed plans for the last week of CASP will be published next Saturday. At this point we want to announce that we will have targets every day Monday through Friday, and that there will be no more RNA targets released.
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| CASP15: week 11 (July 11-17) | (2022-7-9) |
Dear CASPers,
We are three weeks away from the end of the CASP15 target release season. After the last two weeks featuring very large structures (3000+ residues) and, as a result, a smaller number of targets, we are back to a more traditional target release schedule. Next week we will release 10 targets (two per day), including six targets for the assembly prediction. There will be no RNA and at the most one ligand prediction target.
CASP organizers
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| T1170, H1171 and H1172 for assembly and ligand prediction | (2022-7-6) |
Dear assembly and ligand predictors,
Today we released the first target, T1170, from a series of 3 targets: T1170, H1171 and H1172. These targets represent different intermediate conformational states of the multimolecular complex.
Molecule 1 (RuvB) can assemble into a hexamer, where some of the subunits can accommodate double stranded DNA. This molecule (RuvB) can harbor none (target T1170), one (target H1171) or two (target H1172) molecules 2 (RuvA). Molecule 1 can be in ATPgS, ADP or apo state, and all states can be present in it's oligomeric assembly.
Target T1170 (RuvB hexamer) has one dominant conformation / nucleotide configuration.
Target H1171 (RuvB hexamer + RuvA) can come in two conformations / nucleotide configurations.
Target H1172 (RuvB hexamer + 2 * RuvA) can come in three conformations / nucleotide configurations.
CASP organizers
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| Planned network outage at the UC Davis tonight | (2022-6-29) |
Dear CASPers,
There will be an interruption in the web services at the UC Davis campus today, June 29, in the time window from 5 pm PDT till 2 am tomorrow (June 30). The expectation is that the cutover will last for a much shorter period of time (likely a couple of hours), but please be prepared that at any time during the specified time window you might not be able to connect to our servers and send/receive emails to/from us. If you have a prediction server - please make sure that all the models that you expected to be sent out late today - early tomorrow PDT actually went through. If you do not see a prediction in the Model Viewer, you might want to resubmit it before the deadline. Note that for tomorrow we have two targets expiring - H1143 and T1147.
CASP organizers
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| CASP15: weeks 9 and 10 (June 27 - July 10) | (2022-6-25) |
For the next two weeks we have a similar plan for the target release. Both weeks will see four targets. On Mondays we will be releasing a large target (3000+ residues) for tertiary structure prediction, Tuesdays will be left blank, and Wednesdays through Fridays will see targets with the predictive accent in other modeling categories.
Such a schedule will allow not overloading tertiary structure prediction servers with too many tasks when the large target is in the works. In addition to this, we will allow extra time for predicting these targets (5 days for servers and 4 weeks for humans).
The other three targets from the first week are protein-Fab complexes intended for the assembly prediction (also CAPRI). We will not be collecting subunit predictions on these targets separately.
In the second week, the other three targets are for the assembly and ligand prediction. We will provide additional information on those in due time.
CASP organizers
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| H1164 - canceled after being barely released | (2022-6-24) |
An hour ago we released target H1164 for assembly prediction (also CAPRI). And half an hour ago we received a message from the authors that a preprint of a competing NuA4 structure has just been published (https://www.researchsquare.com/article/rs-1497616/v1). Thus we have to cancel this target.
CASP organizers
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| CASP15: week 8 (June 20-26) | (2022-6-18) |
Next week we will release a series of 5 targets for ligand prediction (apo and one-point mutant holo with 4 different ligands). Even though the Monday target in this series is an apo structure, we encourage dedicated ligand prediction groups to model it as well to be able later to compare unbound and bound-state models.
On Monday, Wednesday and Thursday will have one additional monomeric target for prediction.
On Tuesday, we will release two small multimeric targets with similar sequences but different conformations due to the crystallization conditions (also selected for CAPRI).
On Friday, we will have a huge assembly target (also CAPRI). The target is a 6-unit complex of around 7000 residues total. Five out of six units have 100% hits to the PDB, and the sixth unit has high sequence identity. However the authors warned us that some subunits of the published structure from another group have serious modeling errors and that their own structure cover more residues, essentially solving three new complex components (so - go beyond what you will see in the published structure). We will post links to the related publication and cryo-EM map in the next-week communique.
CASP organizers
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| Re-submission of ligand predictions for 3 targets | (2022-6-15) |
Dear ligand predictors,
We provided wrong ligand tautomeric state for 3 targets: R1117, T1127 and T1146. To remedy the situation, we corrected the SMILES string for target T1146, which is in prediction for two more weeks, and re-released two expired targets as ligand-only targets R1117v2 and T1127v2. Server groups who have submitted ligand predictions on T1146 should resubmit modified ligand predictions by Saturday, June 18 in manual regime. Human groups should re-submit ligand predictions on T1146 by the target human expiration date (June 29).
CASP organizers
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| CASP15: week 7 (June 13-19) | (2022-6-11) |
Dear CASPers,
1. With six weeks of prediction behind us, we have passed the CASP15 equator.
After the outstanding performance of AphaFold2 on single-domain proteins in CASP14, we expected a shift of interest in the prediction community from single proteins to complexes. And that indeed happened. In CASP15/CAPRI, we have 81 groups participating in the assembly category compared to 49 in CASP14. That's a 65% increase!
The participation in the single-protein prediction continues to be very strong with 127 groups sending models. This represents only 15% drop from the previous CASP (149 groups in CASP14). At the same time, we are happy to welcome new groups coming to the field, mainly from the AI community. A teaser: first evaluation results show that some single-protein targets still constitute significant predictive challenge and that the accuracy of AlphaFold2 models can be surpassed. Thus, the single-protein prediction category is very much alive and still worth investing your time.
The accuracy assessment category took a big dip in participation with the switch of the prediction scope from monomeric to multimeric targets. The refurbished category drew attention of 26 groups specializing in assessing accuracy of interfaces and overall multimeric fold compared to 73 groups specializing in accuracy of monomers in CASP14.
Introduction of two new categories, RNA prediction and Ligand prediction, got a great response from the community with 35 and 31 groups participating, correspondingly. At this time, we already secured more than 10 targets in each of these categories allowing us to carry out a meaningful evaluation of the results. We are very eager to determine the state of the art in these prediction areas.
2. Next week plans.
Assembly targets (also CAPRI) will be released on Monday, Tuesday and Friday.
We will have four single-protein targets Mon-Thu, additionally to subunits of the assembly targets. The Wednesday target is on a larger side with ~1400 res. The Tuesday target is a monomer, but we will formally release it as a dimer to allow proper placement of the ligand for those participating in this prediction category.
An RNA target will be released not on Friday as it became usual in this CASP, but on Thursday. Please note that the target has some heterogeneity and you might consider submitting different models (out of 5 permitted) representing alternative conformations.
Andriy Kryshtafovych for
CASP organizers
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| CASP15: week 6 (June 6-12) | (2022-6-5) |
1. This week Monday through Friday, we will have one target per day for assembly prediction. All these targets will also be part of CAPRI. The targets feature an CNPase (structure known) and five different nanobodies. The challenge is predicting the binding site and the complex conformation. These will be assembly-only targets, i.e. no TS prediction for subcomplexes will be requested.
2. Additionally we will have five TS-designated targets spread over the week.
3. As usually, we will also have an RNA target on Friday.
CASP organizers
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| CASP15: week 5 (May 30 - June 5) | (2022-5-28) |
1. This week we will have 9 TS targets spread Mon-Thu, one very large multimeric target (CAPRI) on Friday, and two variants of the same RNA (young and mature) on Friday.
2. Attention QA predictors: today we erroneously sent a duplicated request for estimating accuracy of H1111 models (first at 9:35 and then at 10 am). This is a big target - so please make sure your server does not do the same work twice.
CASP organizers
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| CASP15: week 4 (May 23-29) | (2022-5-21) |
1. RNA update.
At the request of predictors, we started posting server models submitted on RNA targets at predictioncenter.org/download_area/CASP15/server_predictions.
Models for R1107, R1108, R1116 and R1117 were posted yesterday (May 20); models for currently active server targets (R1126 and R1128) and all future RNA targets will be posted at 2pm PDT on the server expiration date. Currently, there are 9 server groups submitting RNA predictions.
2. Next week we will see first targets expiring for human-expert prediction, including a few multimeric targets. This means the time for QA prediction is coming. The QA prediction window for upcoming targets is reported through the Target List page.
3. Plans for week 4 (subject to change).
Monday: 1 target - H1129 (heterodimer/CAPRI, one subunit for TS)
Tuesday: 2 targets - T1130 (TS), T1131 (TS)
Wednesday: 2 targets - T1132 (homomer/CAPRI); , T1133 (TS)
Thursday: 1 target - H1134 (heterodimer/CAPRI, two subunits for TS)
Friday: 3 targets - H1135 (heteromultimer/CAPRI with ligands); R1136v1, R1136v2 (RNA, apo and holo conformations)
CASP organizers
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| CASP15: week 3 (May 16-22) | (2022-5-14) |
Next week we plan to release ten targets, including 4 or 5 multimeric (also CAPRI), 2 with ligands, and 2 RNA (on Friday).
CASP organizers
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| QA prediction in CASP15 | (2022-5-7) |
We want to clarify that QA prediction in CASP15 is requested on oligomeric targets only, and only after all structure models are collected. This differs from previous CASPs, where QA prediction was run on server models submitted on monomeric targets. Tarballs with oligomeric models for accuracy estimation will be posted at our website the next day after closing target's human prediction window. At that time, requests will be also sent to registered QA servers.
Thus, the first QA target in CASP15 will be released on May 26 (H1106), followed by two targets (T1109 and T1110) on May 27. QA predictors will have 2 days to submit their accuracy estimates.
CASP organizers
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| CASP15: week 2 (May 9-15) | (2022-5-7) |
1. In week 1, we released 11 targets in different categories (including two subunits of hetero-complex H1106) and collected over 1,300 models.
2. Some clarifications about the targets released last Friday.
Target H1111 is a target for assembly prediction only. We did not release its individual subunits for prediction as two of them, YscX and YscY, had been released as targets T1106s1 and T1106s2 forming H1106, and the third, YscV, is a domain with known structure (PDB ID 7alw). The challenge here is to model the 9:9:9 complex of YscX:YscY:YscV. Please stick to the target template posted at predictioncenter.org/casp15/target.cgi?id=39&view=all.
Target T1105v1 is a target for server/ligand prediction only. As such, we are expecting protein receptor predictions from servers only (T1105v1 sequence is almost identical to that of T1105, with one-point mutation). The challenge for human-expert groups is to predict this protein mutant in complex with the queuosine ligand.
Targets R1107 and R1108 are targets for RNA prediction. These targets have been also released separately as RNA-puzzles PZ35 and PZ36. Note that future CASP RNA targets will be released through the CASP website only, but will be fully shared with the RNA-puzzles organization. The RNA-puzzles organizers posted the following information about the targets: == The structures have been crystallized and solved using the U1A co-crystallization technique (a loop contains the U1A recognition sequence). In these puzzles, the RNAs form a dimer structure. Please predict each of these two puzzles as dimers. ==
3. Reminding that we are releasing AlphaFold2 and RosettaFOLD models through predictioncenter.org/download_area/CASP15/server_predictions. The models are posted at this address two hours after closing server prediction on the target (i.e. at 2pm PDT).
4. Plans for week 2 (subject to change)
Monday: 1 target (TS)
Tuesday: 1 target (oligo/CAPRI)
Wednesday: 1 target (heteromer/no_CAPRI, subunits, ligands)
Thursday: 1 target (oligo/CAPRI)
Friday: 3 targets including 2 RNA (one with ligand), and 1 TS (with ligand)
CASP organizers
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| No RNA targets for tomorrow | (2022-5-3) |
Two RNA targets that were planned for tomorrow's release (Wednesday) will be released on Friday.
Instead, tomorrow we will release a binary complex of two proteins H1106, and its subunits. This target was also selected for CAPRI.
CASP organizers
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| CASP15: week 1 (May 2-8) | (2022-4-30) |
Dear CASPers,
We have cleaned our databases and the file system after the server test runs, and are ready now to roll CASP15 modeling experiment. The prediction season starts next Monday, May 2 at 9 am PDT.
Eight targets are planned for the first week:
Monday: 1 TS target
Tuesday: 1 TS target
Wednesday: 1 TS target and 2 RNA targets
Thursday: 2 oligomeric targets (both selected for CAPRI)
Friday: 1 TS target with ligand
Plans for the second week will be announced next Saturday.
Good luck,
CASP organizers
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| Ligand prediction in CASP15 | (2022-4-29) |
Dear prospective CASP predictors,
As you had been informed, we are starting a pilot experiment on ligand prediction in CASP15.
Some of the prospective CASP15 targets were solved in complex with ligands /ions /small molecules. If known and likely biologically relevant, the ligand info (SMILES) will be disclosed to you through target pages (similar to https://predictioncenter.org/casp14/target.cgi?id=8&view=all). We encourage predictors to predict poses of the suggested ligands (new LG prediction category) in addition to the protein receptor prediction (TS prediction category). The predictions will be accepted in the MDL format. Please consult our CASP15 format page https://predictioncenter.org/casp15/index.cgi?page=format#LG for the details on submitting ligand predictions.
The first ligand target will be released towards the end of the first prediction week.
CASP organizers
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| AlphaFold2 and RosettaFOLD models in CASP15 | (2022-4-27) |
Dear prospective CASP15 predictors,
We want to inform you that AlphaFold2 and RosettaFOLD models will be available to all human predictors in CASP15 immediately after closing server prediction (typically three days after the target release). The models will be generated by three participating CASP15 servers (af2-standard, af2-multimer and Baker-server) and posted on the Prediction Center website at https://predictioncenter.org/download_area/CASP15/server_predictions. The RosettaFOLD models will be provided directly by David Baker's group, while AlphaFold2 models by Arne Elofsson's group, who will run standard monomeric and multimeric AFv2.2 protocols suggested by Deepmind.
Additionally, the Elofsson group will post a larger set of alphafold-standard and alphafold-multimer models (25 normally) and the corresponding multiple-sequence alignments (MSAs) for all CASP15 targets at http://duffman.it.liu.se/casp15/.
CASP organizers
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| CAID: Critical Assessment of Intrinsic protein Disorder - Round 2 | (2022-4-27) |
A message from CAID organizers:
We have launched the second round of the CAID challenge. The timeline and all relevant information are available at https://idpcentral.org/caid. In CAID2 we added a couple of new categories: the prediction of entropic chains (i.e. linkers) and the prediction of ID binding residues subclasses, i.e. protein binding or nucleic acids (DNA/RNA) binding.
We plan to announce preliminary results at the IDPfun consortium conference (Dublin, Aug 29 - Sep 2), and the final results at the CASP15 conference in December.
CAID organizers
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| CASP15 servers testing: stage 4: QA servers | (2022-4-26) |
We continue testing QA servers on two multimeric test targets - H1046 and T1032. Test queries were sent to the servers yesterday and today. The test will be over tomorrow at noon Pacific Time. Make sure by then that your server is able to send predictions in the required format.
CASP organizers
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| CASP15 servers testing: stage 3: oligomeric servers | (2022-4-21) |
Today we sent requests to the registered tertiary structure and assembly servers for modeling two test multimeric targets: T1032 (homomultimer) and H1046 (heteromultimer).
Please get in touch with us if any problems with the connectivity /format.
QA servers will be tested next week.
CASP organizers
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| CASP15 servers testing: stage 2: RNA servers | (2022-4-20) |
Today we sent a request to the registered RNA servers for modeling a test target R1099.
Please make sure your server sees it and generates prediction(s) as expected. In case of any issues - get in touch with us at casp@predictioncenter.org.
CASP organizers
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| Start of testing CASP15 servers | (2022-4-18) |
Dear CASP15 server predictors,
We have started the first round of checking connectivity and correctness of prediction format for servers registered for tertiary structure prediction. We sent a test target T1031 to all registered servers. If you had registered a TS server, but have not received at least one request from us please check the Server Queries link from the main CASP15 web page to see the status of the queries to your server. In case you notice any problems, please check your registration settings and contact us if in doubt. Also, if you do not see your prediction(s) as accepted in our server status page (link Server Prediction Status) or through the Model Viewer /My CASP15 Profile pages, then either your prediction did not reach us or was rejected due to unregistered with CASP submission email or format issues.
A request to EMAIL-server curators. Please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T1031 - query received by MY_SERVER". Failing to do this may affect the timely addressing of unexpected connectivity failures.
We will continue testing TS servers for two more days.
CASP organizers
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| B-factor field | (2022-4-7) |
Dear method developers,
We slightly modified format of CASP15 TS prediction by requesting atom-level confidence scores in the percentage form (0.00-100.00) instead of originally suggested fraction form (0.00-1.00). This way you will be able to provide increased precision estimates within the PDB format allowing two decimal places in the B-factor field.
CASP organizers
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| Registration for CASP15 has started | (2022-4-3) |
Please go to https://predictioncenter.org/casp15/registration.cgi and register.
CASP organizers
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| April 4 - start of CASP15 registration | (2022-3-22) |
Dear CASPers,
CASP15 registration will open on April 4, server testing on April 18, and the first target will be released on May 2, 2022. The experiment will run May-August and culminate with a conference in Europe in December. Please check the CASP15 web page (https://predictioncenter.org/casp15/) for more details on the upcoming experiment.
Given the tremendous progress of the last two experiments and the clear potential for further progress, especially in the assembly category, we look forward to another exciting experiment. Success will primarily depend on two things: your participation and the identification of targets, particularly for complexes, RNA , protein-ligand, and conformational ensemble prediction. Please help us find suitable targets - talk to your colleagues now.
CASP organizers wish you a successful prediction season!
John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Maya Topf
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| CASP15 call for targets | (2022-3-11) |
CASP (Critical Assessment of protein Structure Prediction) is in search for targets for the upcoming CASP15 modeling experiment (starting in May 2022). CASP community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. Typically, about 100 modeling groups from around the world participate. Results of CASP experiments are assessed by leaders in the field (http://predictioncenter.org/index.cgi?page=assessors_list), and published in special issues of the journal PROTEINS (see https://onlinelibrary.wiley.com/toc/10970134/2021/89/12 for the latest issue).
Following the 2020 CASP14 experiment, it is hard to find a structural biologist who has not heard about the success of deep learning methods in modeling protein structures, particularly by the AlphaFold and more recently RosettaFold. As a result of these advances, computed protein structures are becoming much more widely used in a broadening range of applications. Since CASP14, the protein modeling community has intensified development of these methods and extended their application to include modeling of protein complexes and protein ensembles. CASP15 will provide definitive insight into how successful these new developments are.
CASP15’s success depends on generosity of the experimental community in providing targets as ground truth against which to assess the computation methods. Over the years more than 150 structure determination groups have provided over 1100 targets for CASP challenges. For CASP15, we are requesting submission of all types of experimental structures determined by X-ray crystallography, cryo-electron microscopy and NMR as potential targets, but are particularly interested in the following:
1. High resolution structures of single proteins. Because of the high accuracy of the new computational methods, it is becoming difficult to distinguish experimental error from computational error in low resolution structures.
2. Structures with few or no known sequence relatives. Consistently accurate computed structures for this class of target requires methods that do not depend on evolutionary relationships.
3. Protein complexes. Deep learning methods already show increased performance in this area, and a range of complexes is needed to establish exactly how powerful these are. Assessment will be in partnership with CAPRI, as in other recent CASPs.
4. RNA structures, RNA complexes, and protein RNA complexes. Many more RNA structures are now being determined experimentally, opening this area for more extensive rigorous assessment.
5. Proteins with clearly determined alternative conformations. An obvious extension beyond single protein structures is the calculation of ensembles of conformations. The new computational methods are already being applied to this problem, but there is a paucity of definitive experimental data to assess these against, which may limit this category.
6. Protein-organic ligand complexes. Deep learning methods are also being applied to these structures. We are exploring including this category in CASP15. A major challenge is obtaining suitable targets.
We also plan to include modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, and crosslinking mass spectrometry. For that, protein material is needed (this is not expected for most targets, but if available, it would be much appreciated!).
So, if you have suitable targets in any if these areas, we would very much appreciate you getting in touch by replying to this email or writing to casp@predictioncenter.org or suggesting your target directly through the CASP15 target entry page: http://www.predictioncenter.org/casp15/targets_submission.cgi.
Note that CASP target providers are regularly invited to contribute to CASP special journal issue papers (e.g. https://onlinelibrary.wiley.com/doi/epdf/10.1002/prot.26223, https://onlinelibrary.wiley.com/doi/10.1002/prot.26247), and we plan to continue this practice in the future.
Thank you,
CASP15 organizers
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| UNIPROT survey | (2022-2-16) |
A message from Alex Bateman (EMBL-EBI):
UniProt is considering whether it is useful for our users to provide one or more sequence embeddings across UniProt sequences and how best to do that. We think that the CASP community are one such important use community who could help steer us in the right direction. We have prepared a short survey to help gather interest:
https://docs.google.com/forms/d/1AfAZd9lCDwQ9IxWola2xWFgHpdkOP2He1zyfhUuNpuM
The survey will take about 10 minutes to complete and the aggregated results may be reported in future publications.
Thanks for your help.
- Alex Bateman
- https://www.ebi.ac.uk/about/people/alex-bateman
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| CASP15 plans | (2021-12-6) |
Dear CASP community member:
We are writing to let you know about plans for CASP15. We have extensively discussed these within the organization and with the advisory board. However, what is included in CASP is ultimately determined by what members of the community are interested in doing. We would greatly appreciate your feedback as well as any additional suggestions. We would also very much like your suggestions on how to obtain targets in some of the more difficult areas.
We expect to run the experiment on the usual CASP timetable: targets will be available from approximately the beginning of May 2022 through August, and the CASP conference will be in December.
The core of CASP remains the same: Double-blind testing with independent assessment against experiment to establish and advance the state of art in modeling proteins and protein-complexes.
CASP categories will change: Existing categories will be modified; new ones added (tentatively RNA structure, protein-organic ligand complexes, and conformational variability); and it is proposed that some of old ones (refinement, single protein related accuracy estimates, and contacts/distances) will be dropped. Each of these changes is outlined below. CASP has very limited resources to make these changes, and where appropriate we will explore collaborations.
Single proteins and domains: This category has been the core of CASP and will continue. The AlphaFold2 and RoseTTAFold methods set a very high bar, but it is important that there is further objective testing and analysis. We expect there will be a number of new competitive methods. Assessment is likely to focus more on the conditions under which poorer structures or parts of structures are obtained and whether any modeling methods produce more accurate models in those circumstances.
Assessment will place more emphasis on side chain accuracy. Related to that, as outlined further below, one proposed change is that participant provided accuracy estimates will be required to use lDDT units, not Angstroms as previously, and should be provided for all atoms, not just per residue.
Protein complexes and domain-domain interactions: We already know there will be very substantial progress here, from the availability of more accurate models of component structures, application of newly developed multimeric AlphaFold and RoseTTAFold methods, adaptations of those, and new more specialized deep learning approaches. So, this will be an exciting area in CASP15. Availability of a suitable range of targets remains a challenge, and we ask for your help with that. As in recent CASPs, we plan to again work in close partnership with CAPRI.
Refinement: CASP has long encouraged the development of physics related methods, in the belief that informatics could only get us so far. The CASP14 results appear to show that is not correct - no refinement method, given a typical starting model, could get anywhere near AlphaFold accuracy. Nor could refinement improve the accuracy of AlphaFold2 models. Also, refinement methods are now included in all better-performing methods as part of their pipelines. So, at least in its present CASP format, this aspect of physics-related modeling seems to have run its course. Subject to further input from that community, we propose to drop it. As noted below, there are other physics application areas that now should receive more attention.
Accuracy estimation (EMA): CASP has nurtured the development of these methods for a long time, it is a very important area, it is a popular area, and it has shown lots of progress over the years. However, two limitations became apparent in CASP14. First, it is very difficult to devise methods that perform equally well on all models, irrespective of the model generation method. Second, in the first CASP real life test - selecting which models of SARS2 proteins were most accurate - the methods failed. Also, similarly to refinement, EMA methods have become an integral part of structure modeling methods, and some (for example, AlphaFold2 and RoseTTAFold) have shown very high accuracy.
Thus, we are proposing to discontinue assessment of general accuracy estimation methods for single proteins. Instead, we will focus on assessing self-reported estimated accuracy, both backbone and side chain. As noted above, atomic accuracy estimates should be reported in lDDT units not Angstroms, and should be for all atoms, not just Calphas.
We will also include assessment of estimated accuracy of assembly interfaces, for which there will be a separate submission format. We would like input on this proposal.
Contacts and distances: This is also an area nurtured by CASP for a long time - since 1996 - and it finally paid off big, paving the way for the deep learning approaches. It has also been a popular area. But it is no longer clear it makes sense to separate it out from the overall modeling pipeline. It will be discontinued unless there is extensive community opinion to the contrary.
RNA structure and complexes: We have been approached by some members of the RNA community to include this type of challenge, and have said we will, subject to the availability of targets and resources. Please let us know if you are interested/ready for this type of modeling. The data handling and evaluation requirements are different from protein work, and we are exploring working in collaboration with an appropriate group.
Protein - organic ligand complexes: This is an area where deep-learning is already having an impact, and there is high interest because of the relevance to drug design. D3R used to perform CASP-like experiments in this space, but has now stopped. The new CACHE initiative will include a structural component, but be limited in scope from this perspective. We are exploring whether suitable collaborations can be formed in this area. As part of that, it is likely that results of the latest GCPR experiment will be presented at the CASP conference and there may be other interactions with that group.
Data assisted modeling: There was no data assisted category in CASP14 because of Covid, so momentum has been lost. Also, results so far have been disappointing, and participation has been limited. Further, because of the improvements in unassisted modeling, this landscape has changed. Some previous activities, such as SAXS and chemical crosslink assisted modeling, may still be worth pursuing for large molecules and complexes. Others, particularly sparse NMR data assisted, now seem less relevant.
Since experimental data in this area usually have to be especially generated for CASP, we would like to gauge interest. Please let us know if you would participate in SAXS or Cross-linked assisted modeling.
Note that the next section outlines plans for assessment of conformational ensemble modeling, an area that would be evaluated against these sorts of data.
Disorder, conformational ensembles, dynamics, energy landscapes: With the dramatic solution of the static structure modeling problem, attention has become more focused on non-static structural properties. We are exploring what is possible here, and hope to conduct pilot experiments in CASP15. It is not one thing, and we can see at least four categories, listed below. A primary limitation is the availability of suitable experimental data.
Disorder: CASP used to include a disorder category, based on predicting which regions are not seen in crystal structure electron density maps. That was discontinued partly because it is a poor standard for disorder, and partly because the methods were not improving. Silvio Tosatto now runs a CASP-like experiment (CAID) for which results have been presented in recent CASPs, and it is likely that will occur again.
Conformational ensembles: Silvio is also interested in a pilot experiment in CASP, testing whether participants can produce ensembles that fit experimental data, particularly some types of NMR data, cross-linking, and SAXS. Cryo-EM maps may also be a source of suitable data. We will be consulting with Silvio and our experimental collaborators in these areas to see what might be possible. We would also welcome input and suggestions from other members of the community.
Dynamics: in principle, there could be suitable NMR and other data against which to test more short-range motions, and it is an area where physics related methods have a role. The obvious difficulty is obtaining suitable experimental data. Please let us know if you see any possibilities here. but we have no plans in place at present.
Energy landscapes: For example, alternative minima sampled by some kinases in response to post-translational modification, ligand binding, or physical conditions. Once again, obtaining suitable experimental data is primary issue. We currently have no plans in this area.
That’s it for now. We realize it’s quite a lot of proposed change. So again, we really want your feedback. Please email, but also please put comments on the new CASP15 DISCORD forum (join at https://discord.com/invite/gQgSQkCzH7) and start discussions there.
CASP organizers.
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| CASP14 issue of Proteins is out; CASP15 announcement to come shortly | (2021-11-25) |
Dear CASPers,
1. We are happy to announce that CASP14 special issue of Proteins has been published today:
https://onlinelibrary.wiley.com/toc/10970134/2021/89/12
All articles are publicly accessible. Enjoy a nice Thanksgiving present from Proteins!
2. We want to inform you that in October-November, the CASP organizers conducted a series of zoom calls with the CASP Advisory Board to discuss plans on running the upcoming CASP15 experiment. We are finalizing a document summarizing the suggested changes and hope to be able to share it with you in a week or so.
Happy Thanksgiving!
(for those who does not know what it is - it is a big Holiday in the USA starting today; in particular it is a good occasion for us to express gratitude to all our supporters all over the world).
CASP organizers
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| GPCR Dock 2021 | (2021-11-12) |
A message from Raymond Stevens:
Happy to announce GPCR Dock 2021, a new round of the community-wide GPCR modeling and docking assessment, organized by UC San Diego and iHuman Institute of ShanghaiTech: https://gpcrdock2021.org/. Please register early and make sure to tell your friends and colleagues!
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| Illumina is hiring Deep Learning/AI Scientists | (2021-11-6) |
A message from Jinbo Xu on behalf of Illumina:
Hundreds of millions of human genomes and exomes are expected to be sequenced over the next decade, driven by steady innovations in sequencing technologies pioneered by Illumina. The enormous quantities of genomic data being generated by Illumina in collaboration with our partners worldwide represents a major opportunity to develop novel data-driven and artificial intelligence methods to extract clinically actionable information from the genome, and apply it towards improving human health.
To accelerate the adoption of clinical sequencing, Illumina is recruiting a world-class deep learning scientist to work on the development of novel deep learning algorithms for deciphering the effects of genetic variants in the human genome. Major aims would include modeling the effects of genetic variants on protein function, and diagnosis of pathogenic variants in patients with cancer or rare genetic diseases.
A key objective is to publish research results in peer-reviewed journals in order to improve the accuracy, throughput, and reproducibility of genome interpretation, thereby removing barriers to clinical adoption of whole genome sequencing. In addition to strong analytical skills, this position will require a high degree of initiative, autonomy, and scientific collaboration.
Responsibilities:
Lead the development of novel deep learning for deciphering the human genetic code, diagnosing pathogenic genetic variants by combining information from detailed clinical phenotypes and medical records, protein structures, and genomic data.
Lead scientific collaborations with Illumina’s academic, nonprofit, and industry partners, and lead a multidisciplinary team focused on achieving these aims.
Publish and disseminate methods and findings and incorporate them into software products to the benefit of the wider genetics community.
Requirements:
Expert in machine learning, statistics, and proteinomics / genomics
Possesses strong communication skills, with the ability to present complex scientific ideas to clinical, scientific, and industry audiences.
Be willing to work in a fast paced, competitive environment, and hold a strong record of successful delivery of complex scientific projects and publications under tight timelines.
Education:
MD or PhD in computer science, genetics, computational biology, or related field.
All listed requirements are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional task and responsibilities
Job application link:
https://illumina.wd1.myworkdayjobs.com/en-US/illumina-careers/details/Sr-Deep-Learning-AI-Engineer_23583-JOB
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| Positions at EMBL Hamburg | (2021-10-25) |
A message from Jan Kosinski:
Dear all,
At EMBL Hamburg, we have two job and fellowship opportunities in the area of structural modeling of large protein complexes based on cryo-EM and other data.
1) Scientific Technical Officer to develop and apply computational methods for modeling based on electron microscopy and other data, with the particular focus on using recent Artificial Intelligence-based modeling tools like AlphaFold and RoseTTAfold. Three years contract with possibility of extension.
Closing date: 21 November 2021, Apply here: https://www.embl.org/jobs/position/HH00206
2) A software engineer willing to apply for the ARISE fellowship (https://www.embl.org/about/info/arise/programme-overview/), which trains scientists & engineers for careers in research infrastructures. The work would focus on developing software that could become structural biology services in the future. Three years contract.
Closing date: 30 November 2021, Apply here: https://www.embl.org/about/info/arise/applying/.
Please check more about:
our lab: https://www.embl.org/groups/kosinski/
our publications: https://www.embl.org/groups/kosinski/publications/
and more details of the job opportunities: https://www.embl.org/groups/kosinski/open-positions/
We offer access to superb computational infrastructure, experimental data from electron microscopy and other techniques, competitive salaries, and excellent working conditions.
Best regards,
Jan Kosinski
--
Group leader at European Molecular Biology Laboratory (EMBL) Hamburg
Joint appointment Structural and Computational Biology Unit EMBL Heidelberg
Group leader at Centre for Structural Systems Biology (CSSB)
c/o DESY, Building 15 (CSSB), Room 02.247
Notkestraße 85
22607 Hamburg, Germany
Phone: +49(0)40 8998-87573
https://www.embl.org/kosinski/
https://www.cssb-hamburg.de/research/research_groups/kosinski_group/index_eng.html
Twitter: @jankosinski
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| Positions in Sweden | (2021-6-20) |
A message from Arne Elofsson:
We have a number of extremely good positions in Sweden with deadlines in the fall. They are tenure track and funded by a new initiative by the Wallenberg foundation with approximately $2M in startup funding. Additional funding will be available to apply for. The main rule is that you have to be within 5 years from your PhD (with additional time allowed for parental leave, military service etc). In total there are 20 positions, with approximately 5 of these relevant to our community (the others are in Precision medicine, evolution and biodiversity, epidemiology and infection biology)
The title of all position is "Assistant professor in data-driven cell and molecular biology", but a slight variation on the descriptions exist (but in principle, you could apply for all (although obviously the best in Stockholm University as I can get you as my colleague).
A general link for all positions can be found here: https://www.scilifelab.se/data-driven/fellows/
Here are links to the five positions
Stockholm University (2 positions)
https://www.su.se/english/about-the-university/work-at-su/available-jobs?rmpage=job&rmjob=15126&rmlang=UK
KTH: A specific focus is the development of methods that take a quantitative approach to cell and molecular biology with potential to give new insights of biophysical relevance.
https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:406593/where:4/
Chalmers:
https://www.chalmers.se/en/about-chalmers/Working-at-Chalmers/Vacancies/Pages/default.aspx?rmpage=job&rmjob=9592
Linköping University
https://liu.se/jobba-pa-liu/lediga-jobb/ (link not available yet)
Interested in more information:
Arne Elofsson
Tel:+46-(0)70 695 1045
http://bioinfo.se/
Email: arne@bioinfo.se
Twitter: https://twitter.com/arneelof
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| Upcoming conferences: Machine learning in structural biology | (2021-6-16) |
Dear CASPers,
We would like to direct your attention to two upcoming meetings aimed to shed additional light on the recent machine learning driven developments in the field.
(1)
August 2-6, 2021, @CIRM, south of Marseille, France. The first is a workshop intended as a small in-person gathering of approximately 40 people, with heavy emphasis on discussion and exchange of ideas. The organizers will accept contributions from all the most relevant areas of machine learning applied to structural biology. Structural biologists interested in these techniques, and people interested in the interface between physics and machine learning, are also very much welcome. Each day will include (i) short presentations from participants, (ii) free time and ad hoc breakout gatherings (proposed by participants), and (iii) structured discussions.
We expect that the presentation section of the workshop will be accessible to outside participants via internet.
If you find this idea compelling, please pre-register ASAP at:
https://conferences.cirm-math.fr/2700.html
As in-person space is limited, participation will have to be approved by the organizers (please answer the two pre-registration form questions). We realize the time is short and will try to answer as soon as possible.
The meeting cost is $200 ($100 students, $1000 industry) plus accommodation charges (€105 per day, including all meals). Accompanying persons are accepted. Payment details will be sent later.
CIRM (Centre International de Rencontres Mathematiques), is located just south of Marseille. CIRM is part of a university campus next to the Calanques national park on the coast of the Mediterranean Sea.
To alleviate some of the costs, we welcome suggestions of possible sponsors.
(2)
January 3-7, 2022, Big Island of Hawaii. The second is a Session at the Pacific Symposium on Biocomputing, titled AI-driven Advances in Modeling of Protein Structure. Papers are accepted on a competitive basis. The deadline for manuscript submission is August 2, 2021.
https://psb.stanford.edu/
https://sites.google.com/view/psb-2022-aisb/home
We hope these will be great meetings and we very much hope to see you there!
Krzysztof Fidelis (University of California, Davis)
Serge Grudinin (CNRS Grenoble)
Elodie Laine (Sorbonne Université)
John Moult (University of Maryland)
Please direct any questions to Krzysztof Fidelis or Sergei Grudinin.
kfidelis@ucdavis.edu
sergei.grudinin@inria.fr
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| An RNA modeling target | (2021-4-26) |
Dear CASP Participants,
For those interested in modeling of RNA structure, we would like to draw your attention to a newly released RNA puzzle (see the message from Chichau Miao and Eric Westhof below). CASP hopes to include the RNA, and possibly RNA-protein targets in the next edition of CASP.
CASP organizers
===
Message from RNA puzzles:
We are happy that a novel RNP structure will appear soon that has been accepted for entering the RNA-Puzzles challenge as PZ30.
We are planning to release PZ30 at 3pm BST on Monday 12th April 2021. You will have 3 weeks for prediction (deadline is 3rd May 2021). Only human prediction will be accepted in this puzzle.
Please send first the confidential statement from the PI of the lab about this new RNA-Puzzle (PZ30).
[Confidential agreement: I will use the provided sequence data for prediction purposes only. I will not distribute the sequences in any form outside my working group.]
There should be no communication outside the lab to anyone and a restricted circulation within the lab also.
The participants need to send us (e.westhof@unistra.fr; zmiao@ebi.ac.uk) the confidential statement before they can receive the sequences.
For RNA-Puzzles, we are currently using the email (ibmc.cnrs@gmail.com) to receive the submissions.
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| CASP14 Job Fair | (2020-12-22) |
Dear CASPers,
Again, many thanks for your participation in the CASP14 meeting (and making it the most attended CASP meeting to date)! One thing that we were not able to make happen this time around was the CASP Job Fair. To remedy this at least in part, we are opening a job ad web page (accessible through the Job Fair link in the CASP website Menu - direct URL https://predictioncenter.org/jobfair). The first ad on the page is for the UC Santa Cruz Associate Teaching Professor position (a message from Prof. Kevin Karplus at the UCSC).
Happy Holidays to all of you from the CASP team!
The Prediction Center
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| CASP14 Program and updates | (2020-11-26) |
Dear CASPers,
As you might have noticed, we had posted the CASP14 conference program online yesterday. It is available from the http://predictioncenter.org/casp14 web page.
The CASP14 results will be released on Saturday morning California time. Please check our website for the updates.
Also note that tomorrow is the last day to buy a Conference access ticket for $50. The fee will go up on Saturday.
Excited to kick off the conference next Monday,
CASP organizers
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| Early registration deadline and instructions for poster uploads | (2020-11-20) |
Dear CASPers,
If you plan to attend the CASP14 virtual meeting, please register. We will have limited capacity to process registrations during the conference and the access to sessions will not be instantaneous. The registration fee will change from the current $50 to $100 starting November 27. Link to register now: https://predictioncenter.org/casp14/index.cgi
Deadline for poster uploads is November 26 (strict). You will have to be registered for the meeting to upload. An upload link will be sent out to registered participants tomorrow.
POSTERS: Instructions for submission
All posters will be available through a special poster viewing webpage that will be accessible at all times during the conference. In addition, during the scheduled poster sessions, presenters will be assigned a breakout room and a time for their presentation. The breakout rooms will be on the Airmeet platform, for which separate instructions will be sent. In the breakout rooms, screen share presentations will be possible.
Files to upload:
Abstract file: Text format. Title, list of authors, one paragraph of text (up to 750 words but considerably less is recommended). Abstracts should be short - their main purpose is to direct attention to the main poster and/or video presentation(s). Authors: First name, Last name, Affiliation.
Poster file: PDF or .jpg (4000x3000 pixels). A maximum file size of 40 MB.
Video poster presentation (up to 6 minutes): Save your presentation as an MP4 file. Slides should be widescreen16x9 ratio which export best to 1080p videos.
Uploaded file naming convention: File name comprised of (1) EventBrite Order #, (2) presenter’s last name, and (3) presenter’s first name.
Abstracts are mandatory. Both media (static poster and video) can be used or just the one of your choice.
Posters will be subject to an acceptance process by a review panel.
Two ways to consider when making your poster video are the PechaKucha (https://en.wikipedia.org/wiki/PechaKucha) or Ignite talks (https://en.wikipedia.org/wiki/Ignite_(event)) presentation styles.
Some helpful tips on planning your recorded talk are available at
https://www.iscb.org/images/stories/ismb2020/downloads/RecordedPresentationGuidelines.pdf
An example of a presentation: https://youtu.be/rbLbb7eOao8
CASP organizers
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| on CASP14 conference | (2020-11-14) |
Dear CASP participants:
Thanks for all the responses to our earlier message, asking for preferences for attending Europe/USA or Asia sessions of the CASP14 conference.
Almost all responses stated a strong preference for the Europe/USA sessions, and nobody had a strong preference for Asia timing. On that basis, we will hold only the Europe/USA sessions. We very much appreciate our Asia area colleagues' willingness to deal with very inconvenient hours, but think it will indeed be a much better conference with your direct participation.
We will be inviting participants to create extra discussion sessions, both during the meeting period and afterwards. So it will be possible for those interested to hold additional 'local' sessions at more favorable times, if you wish.
Looking forward to seeing everyone in a couple of weeks
CASP organizers.
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| CASP14 online conference registration | (2020-11-6) |
A registration link for the online CASP14 conference is now available from the main CASP14 web page (https://predictioncenter.org/casp14). Members of the assessment teams should contact the organizers prior to the registration. Purchasing the registration also allows presenting a poster at the conference. Details for poster uploads will be provided shortly.
CASP organizers
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| CASP update | (2020-11-3) |
Dear CASPers,
Starting last week and finishing this Monday, the CASP organizers had a series of online meetings with the assessors to hear the results of their analysis of CASP14 submissions. Some exciting results were reported and we are anticipating a very interesting conference! The assessors also suggested groups who should give talks at the conference. We expect to begin notifying selected speakers by the end of the week. The assessors have now been given the list of group identities (also available on the CASP14 web site) and may follow up with questions to individual participants.
We are currently working on the conference program and hope to have a working version by the end of next week. Registration for the conference should open by the end of this week. We will be requesting that all participants pay a nominal registration fee of $50 USD to cover expenses for the online tools used for conducting the conference. Stay tuned.
CASP organizers
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| The CASP14 Conference | (2020-10-1) |
Dear CASP community member:
As you no doubt realize, we will have to hold the CASP14 conference virtually. We are planning to do that from November 30th through December 4th. There will be a limited number of talks each day, lasting a total of not much more than 3 hours. All talks will be pre-recorded, and each session will be repeated to accommodate different times zones. Suggested session times are 16:00-19:30 CET for Europe and the US and 10:00- 13:30 JST for Asia. There will be separate local questions and discussion. We plan to make ‘posters’ and asynchronous interactions as effective as possible.
To compensate for the shorter and likely less intense meeting, we will encourage ongoing interest groups activities afterwards, and there will be a follow-up in-person meeting next summer, CoViD permitting.
We are still deciding the conference details, and would welcome suggestions on how to organize specific aspects of it, based on your own experience of virtual meetings and your preferences. Please include experience with handling a wide range of time zones, and tell us about any useful software and poster arrangements you have encountered.
CASP organizers.
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| CASP14 - week 16 (Aug 31- Sep 6) - Collecting methods abstracts. | (2020-9-1) |
1. Today we released the second of the two promised NMR-assisted targets, N1077. The data are provided at http://predictioncenter.org/download_area/CASP14/extra_experiments/. This concludes all target release in CASP14.
2. Now, when majority of CASP14 activity is over and the assessors started their work, it is time to submit write-ups of your CASP14 methods. We have opened a web page for collecting the extended abstracts. The submission deadline is September 15, 2020. Please read the instructions carefully (in particular those pertaining to formatting the first line of the Abstract) and address all the questions specified in the Abstract submission form (https://predictioncenter.org/casp14/abstracts.cgi).
3. As we announced earlier, CASP14 predictors' meeting will be online. Format of the meeting and dates of the sessions will be announced later this month. A program of the meeting will be available only after the assessors complete their analysis of models (tentatively, in November 2020).
CASP organizers
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| CASP14 - week 15 (August 24-30); two NMR-assisted targets | (2020-8-25) |
1. TS /RR
Today (August 25) we closed the last CASP14 target in the tertiary structure /contact prediction categories. All in all, we collected around 48,000 predictions in these two categories.
2. Assembly
The last assembly target, H1103, will be closed this Saturday. Around 1,500 predictions have been submitted in this category to date.
3. QA
Accuracy estimation predictions were wrapped up on August 16 with a total of ~11,000 predictions.
4. Refinement
All CASP14 refinement targets have been released for prediction. We will continue accepting predictions on open targets until September 11.
5. NMR-assisted targets
Today we released the first out of two NMR-assisted targets (N1088). The data are provided at http://predictioncenter.org/download_area/CASP14/extra_experiments/. The second target will be released by the end of the week, tentatively on Thursday. This will end up all target release in CASP14.
6. We will start collecting Methods Abstracts next week and will be collecting them until September 15. Please start preparing abstracts already now so you will have enough time to meet the deadline.
CASP organizers
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| CASP14 - week 14 (August 17-23) | (2020-8-18) |
1. The deadline for T1099 has been extended until August 25 to allow more time for multimeric predictors.
2. We are continuing releasing refinement targets through the end of this week. The last CASP14 refinement target will be released on Friday, August 21.
3. We are hopeful that we will be able to release two NMR-data assisted targets early next week. This will end all target release in CASP14.
CASP organizers
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| SARS-CoV2 domains for EMA | (2020-8-12) |
Dear QA predictors,
We released first two out of five CASP-covid QA targets today. The remaining three targets will be released tomorrow and on Friday.
All these targets are domains, i.e. they cover only portion of the whole SARS-CoV2 protein. However, we provided the whole sequence for them as sequence templates, in order to keep consistent residue numbering in the sequence templates (always starts from 1) and structural templates, which contain only coordinates for residues within the predefined domain boundaries. In such circumstances, it is possible to normalize the global EMA scores by either domain length or whole target length. For definiteness and in order not to over-inflate scores for groups whose TS models contain extra (off-boundary) residues, we ask you to normalize the global scores by the DOMAIN length.
CASP organizers
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| CASP14 - week 13 (August 10-16) | (2020-8-10) |
1. Assembly target H1097, and its tertiary structure prediction subunits T1092-1096.
It was brought to our attention that a Ph.D. thesis describing some aspects of this structure is available online.
To level playing field, we are providing a link to this Ph.D. thesis: (https://www.skoltech.ru/app/data/uploads/2018/05/sokolovamaria_3414_62556_Maria-Sokolova_thesis_2018-4-06-181.pdf) and encourage predictors to check it.
We contacted the provider of H1097 and learned that most of the images in the thesis are models of known RNAP structures solved by other people. The thesis discusses only some fragments of the target structure that were available two years ago. The experimental data for the most interesting subunits of the complex were collected only in spring of 2020, and at the time of this writing the structure is in the final phases of model building, after which it will be refined. We are hopeful that the structure will be ready in time for the CASP14 assessment.
2. Refinement
Two new refinement targets will be released on Monday. Tuesday through Friday we will be re-releasing some of the already closed refinement targets to learn if longer refinement runs lead to more accurate models. These targets will be released with the same starting models as in the first round of the refinement, and will be marked with the 'x1' suffix in their name ('x' for extended).
3. EMA (QA)
This Tuesday we are finishing collecting estimates of model accuracy for regular CASP14 targets. However this will not end the EMA prediction season. After all QA predictions for regular targets are collected, we will release five more EMA targets as announced in the week 8 communique. These additional QA targets will be for SARS-CoV2 refinement targets released at the beginning of the CASP14 refinement season (names starting from R19).
CASP organizers
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| CASP14 - week 12 (August 3-9): end of the regular target release | (2020-8-4) |
1. Oligomeric /tertiary structure /contact prediction.
Today we posted the last target for oligomeric prediction in CASP14. This concludes the CASP14 regular target release. Despite the coronavirus-related disruptions in the experimental lab operations, we were able to secure a diverse set of structures (including many FM or FM/TBM targets) for testing your prediction methods. All in all, 83 targets were offered for tertiary structure /contact prediction and 30 targets for oligomeric prediction (including 17 CASP/CAPRI targets).
2. Refinement.
We will continue releasing refinement targets throughout the next three weeks, however we do not expect more than five new targets in this time span. Besides that, we plan to reopen some of the closed refinement targets for further refinement to learn if longer MD runs can result in better CASP14 models.
3. H1103 (released today)
The last CASP14 target is a probable SARS-CoV2/Human complex. The components of this target are known (Orf3a, PDB:6xdc and HMOX1, PDB:1n3u), thus this is a pure assembly target where no tertiary structure /contact prediction are requested. An overview of this target can be found in our data repository: https://predictioncenter.org/download_area/CASP14/extra_experiments/
4. H1102 (released yesterday)
We have canceled this oligomeric-only target due to the diminishing hope for its structure determination.
CASP organizers
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| CASP14 - week 11 (July 27 - Aug 2), message 2 | (2020-7-28) |
A few additional notes on this week targets.
1. H1097 (released today, Tuesday, July 28)
This target is a heteromeric complex intended for assembly prediction only. As such, it will be assessed only in the multimeric category (i.e. for relative orientation of subunits /inter-subunit interfaces). Individual subunits of this target were released earlier as separate targets (T1092-T1096) and will be assessed in the tertiary structure prediction /contact prediction categories separately.
2. T1099 (to be released on Thursday)
This is a CASP/CAPRI target. The target represents the capsid of duck Hepatitis B virus, which features T=4 icosahedral symmetry with a total of 240 subunits. We invite predictors to submit models containing the minimum number of subunits necessary to define the unique interfaces.
3. T1100 (to be released on Friday)
This is a target, for which homologues have been solved in closed (with ligand) and open (w/o ligand) conformations. An open-conformation structure of this protein has been determined with NMR. However this structure could not help in solving the protein from the X-ray data using molecular replacement, thus triggering speculations that the crystal structure may contain a ligand. The utmost test here would be to see if CASP models can help solve this structure with molecular replacement.
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| CASP14 - week 11 (July 27 - Aug 2) | (2020-7-25) |
1. We are entering the last full week of CASP14 regular target release. This week we will have one regular target per day Monday through Thursday and two targets on Friday. This will leave us with only two more targets (as it stands today) for the overflow week of August 3. There will be more refinement targets next week.
2. Last week some predictors experienced issues with model submission on the large multi-chain assembly target H1060. To allow those CAPRI/CASP predictors to resubmit their models, we are extending the H1060 deadline until next Monday, July 27.
3. To allow sever groups without a large amount of computing resources finishing large last-week targets, we are extending by one day server deadlines for T1093 and T1095.
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| A survey on SARS-CoV2 resources | (2020-7-22) |
Dear CASPers,
Christine Orengo together with Sameer Velankar at the PDBe, EBI, are compiling an article for Briefings in Bioinformatics on 'The impact of Structural Bioinformatics tools and resources for studying the structural biology of SARS-CoV-2'. In this article they want to cover how the bioinformatics community, and the CASP community in particular, are engaged in the related research. If you are providing predictions via on-line resources/sites etc (including CASP_commons), please go to
https://docs.google.com/forms/d/e/1FAIpQLSdB2Ud9-CLlSWrXeLhRBcPMHH7layuWAbO36e9-GD2w6jjvOw/viewform
and complete the survey therein.
CASP organizers
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| CASP14 - week 10 (July 20 - July 26) and week 11 (July 27 - Aug 2) | (2020-7-18) |
1. Tertiary structure /Assembly /Contacts
We are approaching the end of the regular CASP14 season. Only two full weeks of prediction are ahead of us. As of today, we have 13 targets left, with one or two more still probable. We can potentially release them in two weeks, but since the majority of the remaining targets are large, we prefer to release only one target per day in the coming two weeks. The remaining targets (3 as it stands now) will be released in the first week of August. There will be no CAPRI targets next week, and one target (probable) the week after that.
2. There will be 5 refinement targets next week.
3. As you might have noticed, we released our first data-assisted target on Friday, S1063. The SAXS data for this target came from the author of the structure, so they may be in slightly different format than those released in CASP13, even though we tried to prepare the data in the form close to that of CASP13. This target is interesting in the way that it has not been solved yet, even though the crystallographer working on it has collected good experimental data. We hope that CASP models (especially data-assisted for the multimeric complex) can help solving this structure. As it stands now, we do not have more data-assisted targets for you this month, however it is possible that we may obtain a few more next month.
CASP organizers
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| CASP14 - week 9 (July 13 - July 19) | (2020-7-11) |
Notes on the previous week targets.
1. T1080 - only 133 residues.
We learned that the structure of this target contains only 133 residues out of the 922 posted. So, the predictors can save their resources by concentrating on modeling residues 649-781. If you are doing multimeric modeling - all chains of the multimer are restricted to the specified residues.
2. H1081 - assembly only.
This target is a homo-multimeric A20 structure that will be evaluated only in the assembly context. Related structure of a decamer exists, so the challenge here is to predict the interface between the stacked decamers and to model the precise fold.
Plans for the next week - 8 targets:
Monday - 2 targets, including one CAPRI
Tuesday/Wednesday - 1 target
Thursday - 2 targets, including one CAPRI
Friday - 2 targets
CASP organizers
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| T1061 - extended deadline | (2020-7-8) |
Since target T1061 is not only large (949 res) but also trimeric, we are extending its prediction window for one more week to allow more time for thorough modeling.
CASP organizers
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| CASP14 - week 8 (July 6 - July 12) | (2020-7-6) |
We are entering week 8 of a typical 11-week CASP regular prediction season with 60 tertiary structure prediction targets released and over 38,000 models collected. This week we will release 6 targets for tertiary /assembly prediction and one target (H1081, on Friday) for assembly only. Two targets (T1078 on Tuesday and H1081 on Friday) are also designated as CAPRI targets.
Refinement targets will be released on the typical schedule. We are finishing accepting CASP-covid originated refinement targets this week and are planning on releasing the collected models for estimation of model accuracy soon thereafter. There will be 5 QA targets of this type, each corresponding to a refinement target staring with R19.
CASP organizers
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| CASP14 - week 7 (June 29 - July 5) | (2020-6-28) |
Notes from the previous week
1. Target H1046 cancellation.
Last week we learned that target H1046 was scheduled for release by the PDB three days ahead of its planned CASP prediction deadline. We tried to save the target by moving its deadline prior to the PDB release date (June 23). However, this did not fully help as we learned that a paper describing the complex was published online a few days earlier (June 17, https://www.sciencedirect.com/science/article/pii/S0022283620304095). Since the vast majority of H1046 predictions were received after June 17, we are forced to cancel this target. Even so, we do not plan to immediately cancel the subunits of this target as around 2/3 of all the received predictions were submitted before June 17. Assessors will carefully inspect the predictions and their submission dates and will make a final decision in due course.
2. Refinement targets with multiple starting models.
Last Friday we released two refinement targets (R1040v1 and R1040v2) that correspond to the same regular target, T1040, but different starting models. In previous CASPs we learned that some targets are more refine-able than others, even though reasons for that were not always obvious. By taking out of the equation the target refine-ability factor, we hope to better understand the extent to which the final refinement result depends on the accuracy of the starting model. Note that for such double-starting targets we will not be revealing accuracy of starting models or location of the areas needing most attention. We plan to release several refinement targets of this kind in CASP14, with the next one coming out already this Monday.
Plans for the next week
Monday - 1 target (CAPRI)
Tuesday - 1 target
Wednesday - 1 heterocomplex and its subunits
Thursday - 2 targets, including one CAPRI
Friday - 1 target
We will continue releasing refinement targets at the rate of one target per day. If double-starting targets will be released in one day, their expiration dates will be spread in time, whenever possible.
CASP organizers
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| CASP14 - week 6 (June 22-28) - Follow up | (2020-6-20) |
To decrease the number of targets expiring on June 23, we are moving the prediction deadline for two targets that were originally scheduled to expire on June 23 (T1042, T1043) to June 26 (i.e., three days later).
CASP organizers
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| CASP14 - week 6 (June 22-28) | (2020-6-20) |
Week 6 plans.
1. We have moved the deadline for targets H1046, T1046s1 and T1046s2 to June 23, which is three days earlier than originally scheduled. The structure of this complex will be publicly released by the PDB next week.
2. Next week we will have:
Monday - 2 targets (including one CAPRI)
Tuesday - 1 heterocomplex and its subunits
Wednesday - 1 heterocomplex and its subunits (CAPRI)
Thursday - 2 targets
Friday - 1 heterocomplex and its subunits (CAPRI)
3. We will continue releasing refinement targets at the rate of one target per day.
CASP organizers
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| CASP14 - week 5 (June 15-21) | (2020-6-12) |
Week 5 plans.
Monday through Wednesday we will release two targets each day, including one for CAPRI. On Thursday and Friday we will have sub-complexes of a large heterocomplex, including at least one more CAPRI target.
Last week our predictors saw first three refinement targets selected from those modeled in the CASP-covid experiment (names starting from R19). We are reminding that that these targets are open for prediction not only to our refinement registrants, but also to all CASP14 predictors. We will see two more refinement targets of this type on Monday and Tuesday and then we will start releasing refinement targets selected from among those released earlier in the regular CASP14 experiment.
Last week three large targets (T1050, T1052 and T1053) were released on three consecutive days causing increased load on automatic servers. In order to allot the servers extra time to process these large targets, we are extending server prediction deadline for two of the three targets (T1050 and T1051) for one extra day.
CASP organizers
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| CASP14 - week 4 (June 8-14) | (2020-6-5) |
Week 4 plans.
On Monday we will release a heteromeric complex. We know that the complex has 1:1 component ratio, but a higher copy number N, which we do not know. So, besides predicting a hetero-dimer, another interesting thing would be to predict the whole complex as a homo-N-mer of hetero-dimers.
Tuesday and Wednesday will see two targets each; Thursday and Friday only one.
CAPRI participants will get two targets to predict on Wednesday and Friday.
In consultations with the EMA community and the refinement assessor, we are in the process of selecting targets for refinement from those modeled in CASP-covid. Once we come to an agreement (tentatively early next week), those will be released for prediction. Note that these targets are open for prediction not only to our refinement registrants, but also to all CASP14 predictors. The principles of how these targets will be assessed will be worked out by the assessors.
CASP organizers
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| CASP-covid structure modeling - next steps | (2020-5-30) |
The results of the second round of modeling for selected SARS2 proteins are now in. Thirty three groups submitted a total of almost 1,500 models, and 23 groups provided accuracy estimation on these. The Round 2 models are available for download (https://predictioncenter.org/download_area/CASPCOMMONS/2020_COVID-19/TS_predictions/stage2/) and the initial analysis is up on the CASP-covid site: https://predictioncenter.org/caspcommons/models_consensus2.cgi.
As you know, the expectation is that in the second round, participants will have taken advantage of identified domain boundaries and membrane spanning regions, removal of a signal peptide, and several apparently under-utilized templates. (Details of these are in included the first round summary document in Microsoft Teams). In addition, consensus methods could take advantage of the sets of Round 1 models.
We are now soliciting input and discussion of the Round 2 results on Microsoft Teams site:
https://teams.microsoft.com/l/team/19%3ab6e5c75880624485a20f4fc103f79065%40thread.tacv2/conversations?groupId=df00ce43-99c4-4d95-a85e-f53f99b74d7a&tenantId=a8046f64-66c0-4f00-9046-c8daf92ff62b .
How good are these models? What are they good for? Are the accuracy estimates reliable. In particular, which are likely sufficiently accurate that they are suitable refinement targets in CASP14? Your participation in this discussion is needed!
CASP-covid
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| CASP14 - week 3 (June 1-7) | (2020-5-29) |
Week 3 plans.
On Monday and Tuesday we will release final domains from the RNA polymerase that we started predicting this week.
On Thursday and Friday we will have two heteromeric targets (one CAPRI) together with their subunits.
On Wednesday we will finish the polymerase by suggesting the whole structure for prediction (~2,200 res). Even though this is a monomeric target, we will be assessing models similarly to those submitted on oligomeric targets. In other words, we will not be assessing accuracy of prediction on individual domains (as these will be evaluated separately), but rather assess ability of predictors to correctly arrange the domains in a complete structure. To distinguish this target from other monomeric targets, we will assign it a target name starting from H (like for hetero-meric targets). We will be sending requests for automatic modeling of this target only to servers registered for multimeric prediction. Contact predictions will not be assessed for this target, but rather for individual domain targets (i.e., T1031, 33...). If you have a multimeric server that also does RR prediction, please make sure that it does not send us an RR prediction for this target, especially the whole distance map as this will have taken around 2,500,000 lines of text, which translates into files around 200 MB in size - no email client will handle files this big. In general, it is a good idea to limit your contact predictions to 50,000 lines with only the most important and reliably predicted contacts included.
CASP organizers
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| Target H1036 | (2020-5-26) |
Dear predictors,
Tomorrow we will release the first CASP14 hetero-meric target - H1036, a virus protein (trimer) with bound Fab fragments. This complex was also picked as a CAPRI target T165. Please note that subunits of this target are either known structures or expected to be reliably modeled with template-based modeling. The main modeling challenge for this complex is to get Fab binding sites right and correctly model the relative orientation of subunits. Due to the nature of this target, we are not asking predictors for intra-chain contact predictions, however you may consider submitting inter-chain contacts.
All in all, there will be 3 targets tomorrow: another domain from an RNA polymerase (T1035); a multimeric complex H1036; and its first subunit (chain A) T1036s1, which will be designated a server-only target and thus will not require RR prediction.
We will have only one target on Thursday (yet another domain from the polymerase), and two more targets on Friday.
CASP organizers
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| CASP14 - week 2 (May 25-31) | (2020-5-23) |
Dear CASPers,
Have you missed CASP? We bet you did. Even amidst the coronavirus disruption of normal life, we are seeing a strong registration for CASP14, with 240 prediction groups declaring their intent to participate. 65 of these groups (including 54 servers) have already sent us their first predictions. In all, by the end of the first prediction week we have already collected over 1,300 tertiary structure predictions and 200 contact predictions on seven single-unit targets. The real time statistics of the CASP14 experiment can be found at https://predictioncenter.org/casp14/numbers.cgi.
Announcements.
1. We have ended accepting CASP-covid QA predictions for the stage2-generated models today (Saturday, May 23).
2. Also today (at 12:15 pm PDT), we have sent first queries to the registered EMA servers. We will be collecting model accuracy estimates on the first CASP14 target, T1024, through May 25 (stage1 QA), and May 27 (stage2 QA).
3. The majority of server tertiary structure predictions (150 models selected for QA-stage2) will be posted at our data archive (https://predictioncenter.org/download_area/CASP14) on the 7th day after the target release (i.e., May 25 for T1024). All server models (including tertiary structure and contact) will be posted at the same place two days later.
4. Next week we are planning to release 10 single-sequence targets (some homo-multimers) and one heteromer. Two of these targets are selected for CAPRI-50 experiment by the CAPRI organizers. These targets will be marked with an asterisk next to the target name in the CASP Target List (https://predictioncenter.org/casp13/targetlist.cgi).
5. Five odd-numbered targets in the next week's release (i.e., T1031, 33, ...) are constitutive domains of a large RNA polymerase (over 2,000 residues). CASP organizers are already in possession of coordinates for this structure, and together with the FM assessors analyzed it and cut into domains for prediction. We want to emphasize that a preprint of the paper describing the structure is available at BioRxiv. However, the organizers and the FM assessors concluded that the ribbon diagrams shown there cover only about 550 residues of the structure leaving about 1,600 largely un-compromised. We decided to proceed with the prediction of the selected domains, disclosing the available information to all predictors. Link to the BioRxiv paper will be provided in the Additional information for every prediction target emanating from this protein.
CASP organizers
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| QA for stage2 of CASP-covid (2) | (2020-5-21) |
Dear CASP-covid predictors,
We delay QA submission for CASP-covid for one day and will start collecting QA CASP-covid predictions tomorrow, May 22 at 9 am PDT. Please remember to send your predictions through the web form and not through the direct email.
CASP organizers
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| QA for stage2 of CASP-covid | (2020-5-18) |
We have posted predictions from the second stage of CASP-covid experiment at https://predictioncenter.org/download_area/ CASPCOMMONS/2020_COVID-19/ TS_predictions/stage2.
We will be collecting model accuracy estimations on the submitted structure models from Thursday May 21 till Saturday May 23. Please submit your QA estimates by using the CASP_commons prediction submission page - please pay attention that you use the CASP-covid (and not casp14) infrastructure to submit the CASP-covid QA predictions.
CASP organizers
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| End of CASP-covid stage 2; start of CASP14 | (2020-5-17) |
Dear CASPers,
1. We will stop accepting stage2 CASP-covid structural predictions at 6 am PDT on Monday, May 18. All collected predictions will be posted to the Prediction Center's Data Archive the same day. The mechanism for submitting stage2 CASP-covid QA predictions will be announced shortly.
2. The CASP14 prediction season will start at 9 am on Monday, May 18. In the first week, we are releasing seven targets - one on Monday, Wednesday and Friday, and two (including one server-only) on Tuesday and Thursday. Please remember that server-only targets are usually selected from among easier-to-predict structures, so they are intended for prediction by server groups only. Please also remember that contact predictions (RR) are typically assessed on harder targets only, so there is no need to submit contact predictions on server-only targets even for server groups.
3. Plans for the second week of CASP14 will be announced next Friday.
Wish you a successful prediction season,
CASP organizers
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| End of server dry run; stage2 of CASP-covid; start of CASP14 | (2020-5-13) |
Dear CASPers,
We are finishing testing CASP14 servers today and will be switching our main attention to the CASP-covid project in the next 4 days. If you still want to register a server for CASP14, we will do our best to make sure the server is correctly configured to communicate with our distribution server in the first days of CASP14. No more server communication tests will be carried out this season.
The CASP-covid system will be re-opened for collecting models tomorrow. We are expecting refined /updated models on seven whole targets from the first round and on separate domains for six of them (see our previous message for domain boundaries). We will be collecting models through Sunday May 17, 11:59pm PDT, when the system will be closed and switched back to accepting CASP14 predictions.
The CASP14 season will start on Monday, May 18 at 9am PDT. As of today, over 200 groups have registered, including 74 servers. If you are planning to participate, but have not registered yet - please do so asap. At this time we also encourage CASP participants to update their Prediction Center accounts and change their passwords through 'My Personal Data' link in the left-hand side Prediction Center Menu (available only if you are already logged in). Those planning to participate in the CASP14-CAPRI50 experiment are required to register both with CASP14 and CAPRI, but the models should be sent only to one gateway. If you send your models to CAPRI, please include your CASP xxxx-xxxx-xxxx group id in the submission as your models will be immediately forwarded to CASP and checked for format compliance.
In the first week, we will be releasing only monomeric targets. Their difficulty will range from easy TBM to more difficult. First multimeric targets will be released starting May 25. At that time (or soon thereafter) we also expect to release first refinement targets based on the domain models obtained in the second round of CASP-covid experiment. These refinement targets will be a part of CASP14 evaluation, provided their structures are solved in time for the assessment.
Good luck!
CASP organizers
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| Second round of CASP-covid | (2020-5-6) |
Dear CASP-covid predictors,
After consultations with our community and CASP14 free modeling assessors, we are announcing second round of prediction for tentative domains of six first-round targets. The suggested targets and their domain boundaries are as follows:
From nsp2 : C1901d1: 1-359; C1901d2: 360-499; C1901d3: 500-638
From nsp4 : C1902d1: 1-32 + 279-400; C1902d2: 33-278; C1902d3: 401-500
From nsp6 : C1903d1: 1-220; C1903d2: 221-290
From PL-PRO : C1904d1: 1-151; C1904d2: 152-317; C1904d3: 318-686
From ORF3a: C1905d1: 1-130; C1905d2: 131-275
From M-protein: C1906d1: 1-103; C1906d2: 104-222
Please note that the second round is open to everyone and not only the participants of the first round. We ask the community to start modeling the suggested domains immediately. Since we are currently working with curators of CASP14 servers on their servers' connectivity and format correctness, the system for accepting predictions will be not immediately available. Once we are done with testing servers (May 14), we will have opened the CASP_Commons infrastructure for accepting CASP-covid predictions. The window for submitting CASP-covid predictions will be open for three and a half days until May 17, 11:59pm PDT. The regular CASP14 prediction season will start on May 18 at 9am PDT.
We want to inform the community that there were interesting and informative discussions of the first-round targets and predictions at two Zoom conferences last week. Some of the insights from the participants have been posted to target-related channels of the CASP-covid Microsoft Teams. The overview of targets and results presented by John Moult at these conferences is available through the 'How to proceed with the COVID-19 initiative' channel ('Files' tab). Invitation to the CASP-covid MS teams have been sent to registered participants of the CASP-covid experiment. If you did not participate in the first round, but are planning on participating in the second and want an access to the discussion forum - please request it by replying to this email.
CASP-covid
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| CASP14 server dry run has started | (2020-5-4) |
Dear CASP14 predictors,
We have started the first round of checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. We sent a test target T9998 to all registered servers. If you had registered a TS or RR server, but have not received at least one request from us please check the Server Queries link from the main CASP13 web page to see the status of the queries to your server. In case you notice any problems, please check your registration settings and contact us if in doubt. Also, if you do not see your prediction(s) as accepted in our server status page (link Server Prediction Status) or through the Model Viewer /My CASP14 Profile pages, then either your prediction did not reach us or was rejected due to unregistered with CASP submission email or format issues.
A request to EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T9888 - query received by MY_SERVER". Failing to do this may affect the timely addressing of unexpected connectivity failures.
We will continue testing TS and RR servers for two more days.
CASP organizers
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| Start of CASP14 server dry run; changed format for RR predictions | (2020-5-2) |
Dear prospective CASP14 participants,
The registration for CASP14 is under way, and as of now we have already 159 methods (including 59 servers) registered.
We will start checking connectivity and correctness of prediction format for servers in the RR (contacts) and TS (tertiary structure and assembly) categories on Monday, May 4. Testing model accuracy servers (QA) will start after TS predictions are collected and collated into tarballs for the EMA estimation (May 10). If you plan to participate in the server track of CASP14 but have not registered your server(s) yet - we advise you to do that at your earliest opportunity. We will be sending your servers a request to predict a test target, which, obviously, will not be a part of the CASP14 experiment.
We want to emphasize that the RR format for contact predictions has changed. Now you can submit the old-style contact predictions in a 3-column format (cf. 5-column format in CASP13) , or you can submit contact prediction AND distance probabilities in a 13-column format. Please consult our format page (http://predictioncenter.org/casp14/index.cgi?page=format) for prediction format details.
CASP organizers
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| Discussion of covid proteins models | (2020-4-24) |
There will be a couple of Zoom sessions next week to facilitate discussion and idea exchange on the outcome of the first round of modeling. These may also be of interest to members of the CASP community who did not participate in the initial modeling, particularly as other methods, for example refinement and consensus based, may be useful in the upcoming round 2. Please let us know if you will attend one of the sessions:
Tue April 28th: 9AM PDT (San Francisco), Noon EDT (Washington D.C.), 5PM BST (London), 6PM CEST (Zurich), 7PM EEST (Vilnius)
Thu April 30th: 5PM PDT (San Francisco), 8PM EDT (Washington D.C.), Fri May 1: 8AM CST (Beijing), 9AM JST (Tokyo, Seoul), 10AM AEST (Sydney)
by filling out the form here:
https://forms.gle/No61bGkTc5f6RFB69
We will send zoom invitations to all registered participants 15 minutes before the meeting start.
The first-round results are very interesting, and preliminary analysis suggests there is a lot to discuss. Examples: For some targets, previously non-obvious domain boundaries are apparent, and these may assist in getting improved models in the second round. For two targets it appears that partial templates were not usually leveraged. For two of the small targets, there is consensus on conformation but these do not appear to be compatible with proposed host protein binding sites. The degree of agreement in conformation varies widely across targets, but in a number of cases, there may be extensive scoop for the use of consensus approaches.
CASP-covid
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| CASP-Covid modeling, stage 2 | (2020-4-17) |
Dear CASPers,
There was great participation in the first round of SARS-CoV-2 protein structure modeling (~1,600 models from 52 groups) and accuracy estimation (~300 estimate sets from 30 methods). A more detailed information on the participation can be found here: http://predictioncenter.org/caspcommons/groups_info.cgi. Submitted TS and QA models are available for download at http://predictioncenter.org/download_area/CASPCOMMONS/2020_COVID-19/. We are working on calculation of the consensus between the received models and are finishing the infrastructure for presentation and analysis of these data and the accuracy estimation data. Consensus results are being posted to the web as they are calculated: http://predictioncenter.org/caspcommons/models_consensus2.cgi. We expect to have a full set of the results on the web by early next week.
The first ten CASP-covid targets are all difficult modeling challenges, and as expected there is often considerable variation between model structures. But visual comparison of the first-round models shows very interesting patterns and alternatives. For the larger targets, some consistent domain boundaries are apparent and there are specific alternative topologies for some domains. All of which suggests a second round of modeling that builds on these results will be rewarding. A Microsoft Teams site to discuss the results has been setup, with a channel for each target. Invitations will be sent out to active participants shortly.
We propose to run the second round of modeling as follows: Two weeks for community analysis and discussion of the models, followed by a two-week window for model revision, with model submission between May 14th and 17th (CASP server testing between May 4th and 13th restricts the submission window). First and second round models will not be considered CASP14 submissions. However, we do propose to include CASP-covid targets as official refinement targets early in the CASP14 prediction season (now scheduled to begin on Monday, May 18). There is no restriction on starting with the selected model, and additional submissions will be strongly encouraged. Of course, we don’t know which of these structures will be obtained experimentally within the CASP14 season, but expect that some will.
We hope that this overall four-step process (initial models; accuracy estimations, comparison and discussion; revised models; and refinement) will be an effective framework for leveraging our advantages as a community. We anticipate that the results will form the basis of a joint publication (all participants as authors) and a session at the CASP meeting.
We are working on preparing an additional set of targets with host proteins. Because of the timing, these will be released as CASP14 targets. We would welcome suggestions on best target choice (individual and complexes). We would also very much welcome feedback on this plan. Contributions can be communicated directly to the organizing committee or through the general Microsoft Teams discussion.
Thanks to all who have taken part so far, a really worthwhile endeavor!
CASP organizers
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| First round of collecting CASP-covid predictions is over - time for the EMA round | (2020-4-6) |
We have finished collecting tertiary structure predictions for the first set of the covid-19 related targets. Overall, the response was good with 1,635 predictions submitted (or 163 predictions per target on average). The predictions have been made available through the CASP Archive web place: http://predictioncenter.org/download_area/CASPCOMMONS/2020_COVID-19/predictions_04.06/
We ask now model accuracy predictors to pull the submitted models from the provided URL (above), run their EMA tools and submit the accuracy estimates to CASP_Commons before April 12. The format for submitting QA estimates is the same as in CASP proper, but please make sure that you designate your QA submission as 'MODEL 2' (see the CASP QA format requirements here: http://predictioncenter.org/caspcommons/index.cgi?page=format#QA).
CASP organizers
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| CASP Update (2) | (2020-4-2) |
As you know, we recently canvased the CASP community on whether or not to delay the CASP14 experiment. Responses were roughly equally split between going ahead on schedule and delaying for a short while. There were very few people in favor of a year’s delay.
On that basis, we have decided to reset the start of the regular CASP prediction season to May 15. The dry run for servers will start on May 4. Because we expect fewer targets (still estimating ~50, with a good proportion of free-modeling ones) the delay should not affect the rest of the timetable. Of course, whether the CASP14 conference will take place in early December as planned is not clear yet, but we do expect to have completed assessment by then, as usual.
We have also discussed whether some aspects of CASP should be omitted this round. As far as we can see, the only area where that will be necessary is data-assisted modeling. The problem here is that material is unlikely to be available for many targets, and the labs that would normally use that material to collect data are shut-down. So we will continue this category on a rolling basis, releasing any targets as the data become available, and where possible allowing an extended period for submission of data-assisted models. We do want to keep this category alive, and so expect to be assembling training and testing sets for participants to use in further developing their methods, especially for modeling of complexes.
An advantage of the delay is that it allows more time for the CASP-Covid experiment. Response in the initial modeling round has been good, and we will be moving on to an accuracy estimation and analysis round immediately after the April 5th deadline, followed by a model improvement and refinement round. We also expect to release a second set of targets, primarily for host interaction proteins and complexes. We also expect some of the CASP-Covid targets to be re-released for prediction in CASP14 proper.
CASP organizers
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| First batch of COVID-19 predictions | (2020-3-26) |
Dear CASPers,
Some of you asked for the immediate release of server models submitted to CASP_Commons SARS-CoV2 experiment. We have released these models through our Data Archive: http://predictioncenter.org/download_area/CASPCOMMONS/2020_COVID-19/server_predictions_03.26/.
These are mainly server models, but some are those received from expert groups between March 18 and March 26.
We do not plan to run the accuracy estimates on these subsets of models. Instead, we plan to release all models for EMA after they will have been received by the all-group prediction deadline (April 5).
CASP organizers
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| CASP and Covid-19 | (2020-3-20) |
Like every other aspect of life, Covid-19 is impacting CASP.
First, as you know, we have launched a CASP modeling initiative for appropriate SARS-2-Covid proteins: http://predictioncenter.org/caspcommons/index.cgi.
Response to that has been strong, with 56 groups registering as of today. We have also received positive and useful feedback from a number of people on the incorporation of refinement, better procedures for comparing and improving first round models, interaction with experimental groups working on structure, and interaction with drug screening activities. More on all this later.
Second, what to do about the CASP14 experiment? The first targets are due to be released on April 15. The shutdown of many experimental labs is likely to limit the number of available targets, although at this point it looks as if a minimum of half the usual number (~50 cf ~100) can be obtained. But there is also the question of the potential impact on computing resources and human resources (for example those now at home with young children). We would like feedback on this from the participant community - should we go ahead as planned, extend the end date of the experiment, or delay until the situation improves? Please send us your thoughts by replying to this email.
Thanks,
CASP organizers
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| Launch of CASP community modeling for SARS-2-CoV proteins | (2020-3-13) |
Following up on our earlier message, CASP has now launched the SARS-2-CoV structure modeling initiative. CASP can make the biggest contribution by generating and evaluating models for the virus’ most challenging proteins and domains - those where there is no experimental structure available and where comparative modeling techniques cannot be used. The goal is to obtain the best possible consensus structures, and, critically, to use the family of models to obtain overall and residue level accuracy estimates. The hope is that these structures will be useful to others for gaining further insight into the virus’ structure and function, for identifying possible epitopes for vaccine development, and for evaluating possible drug targeting strategies. A number of these proteins form part of complexes, and we anticipate a second phase will be generating models of these assemblies.
An initial analysis of the SARS-2-CoV protein sequences using the CASP target analysis pipeline finds 10 proteins and domains that fit the criteria for template free modeling. We now invite members of the CASP community and others to generate and submit models on these targets. The project will use the previously established CASP_Commons community modeling infrastructure:
CASP_Commons: http://predictioncenter.org/caspcommons/index.cgi
Target page: http://predictioncenter.org/caspcommons/targetlist.cgi (click the 'Round 2 (2020)' link at the top of the Target List page for the list of only Round 2 targets)
Registration (if you have not previously registered for CASP_Commons):
http://predictioncenter.org/caspcommons/registration.cgi.
Checking what CASP_Commons groups are already registered under your account:
http://predictioncenter.org/caspcommons/groups.cgi.
Please note that if you register a server group, there will be no queries sent to your server from the Prediction Center like in regular CASPs. Therefore, submit a query to your server yourself and make sure that we have received your server's prediction by the server deadline (March 18).
Subject to feedback from participants, we propose an initial three-week period for model submission, ending April 5th. The first round of model comparison and accuracy analysis will be performed thereafter, in consultation with the appropriate members of the CASP community. Models and analysis will be publicly released as soon as possible.
This is a community endeavor, and we strongly encourage input and discussion of target choice, analysis methods, and other considerations direct to us.
CASP Organizers:
John Moult, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, University of Basel, Switzerland
Maya Topf, Birkbeck, University of London, UK
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| Modeling COVID-19-related proteins | (2020-3-9) |
These days many of us find messages in our Inboxes regarding the COVID19 spread and actions that have to be taken. CASP organizers are weighing in how the CASP community can help in battling the dangerous virus. As you are probably aware, several modeling groups have already taken on this task, e.g.,
AlphaFold: https://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19
Baker group: https://www.ipd.uw.edu/2020/02/rosettas-role-in-fighting-coronavirus/
SWISSMODEL: https://swissmodel.expasy.org/repository/species/2697049
Zhang group: https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/2019-nCov/
We, as a community, are in position to provide a wider representation of models for the COVID19 targets. In the opinion of CASP organizers, the largest impact can be made for the most difficult targets where models often disagree and where comparing of models from various sources can lead to a better understanding of the prediction robustness. One of the options would be to identify the most difficult for modeling experimentally unsolved COVID19 proteins, release them as 'community effort' targets (through the CASP_Commons gateway), collect the models within the 3-week span, run the collected models through the CASP model accuracy predictors, and publicly post the models with the associated global and local accuracy estimates. This way, models can be potentially used by structural biologists for their functional studies of the virus. We plan to proceed with the plans immediately and will start the CASP_Commons registration in a day or two - please check our CASP14 web site (if you have registered for CASP_Commons before, there would be no need to re-register). A facility for accepting CASP_Commons models will be open as soon as we are ready with the targets (hopefully by the end of the week). We do understand that some of you may not be ready with your methods on a such short notice (especially server predictors), but neither are we with our system - so let us try to move in this fluid situation as fast as we can, from both ends. From the regular CASP evaluation standpoint, we may reasonably hope that some of the structures will have been solved by October 2020, in time for the CASP14 assessment. Thus, we plan to re-release the COVID19 'community targets' as CASP14 targets during the regular prediction season (obviously, if the structures are still unsolved by then) and evaluate the collected models in the fall, if the structures become available.
CASP organizers
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| CASP14 registration is open | (2020-3-9) |
Dear CASPers,
The CASP organizers recently discussed the situation with the coronavirus outbreak and decided to proceed with the plans for the next CASP experiment as previously scheduled. Thus, we have opened the CASP14 registration planning to start the regular prediction season on April 15, 2020. Please go to our CASP14 web page (http://predictioncenter.org/casp14), and follow the Register for CASP14 link. Please read the description of the experiment and familiarize yourself with the format requirements, as some of them may have changed. After the eventful latest CASP experiment, everyone is eager to see how the field advanced in-between the rounds.
Information for server group leaders: we will start dry runs to check server connectivity and correctness of format in the beginning of April. Try to avoid missing the early CASP14 targets by making sure that your servers are registered and tested by April 15. If you have questions or comments about the upcoming experiments - please let us know by replying to this message.
Hoping for an exciting new season,
CASP14 organizers
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| CASP14 to start in early April, 2020 | (2019-12-23) |
Dear CASP Participants,
As most of you know, there will be a CASP14 experiment in 2020.
The first CASP14 targets will be released at the beginning of April (earlier than in the past). Registration and server testing will begin in March. As usual, the experiment will culminate with a conference in December, this time in Europe.
Prediction categories will be as in CASP13 (see the CASP13 section of predictioncenter.org for details). Three points of note:
1. We hope to again to work closely with CAPRI on the modeling of complexes, and will strive to obtain more and better targets. Clearly this is an area where deep learning may next have major impact.
2. The data assisted category will focus more on large proteins and particularly complexes with SAXS and cross-linking data.
3. A planned change is the addition of inter-residue distances predictions as well as inter-residue contact prediction. We will be consulting with the participant community about the best way to do that.
Given the tremendous progress of the last two experiments and the clear potential for further progress, we look forward to an exciting experiment. Success will primarily depend on two things: your participation and the identification of suitable targets, particularly for complexes. Please, please, help find targets - talk to your colleagues now.
Please get in touch with comments, concerns, suggestions.
Best holiday wishes from all of us,
Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, Torsten Schwede, Maya Topf
CASP Organizers
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| Job opportunity at TTI-Chicago | (2019-12-5) |
A communication from Prof. Jinbo Xu:
Research and Tenure-Track Faculty Positions at TTI-Chicago
TTI-Chicago invites applications for the following faculty positions in computer science:
• endowed three-year research assistant professor
• tenure-track assistant professor
• full or associate (tenured) professor
• visiting professor
While we welcome applications from many areas of computer science, we will give preference to candidates working in the following areas:
• machine learning
• computer vision
• natural language processing and speech
• robotics
• computational biology
• algorithms and complexity theory
About TTI-Chicago
TTI-Chicago is a philanthropically endowed academic institute dedicated to fundamental research and graduate education in computer science. TTI-Chicago produces cutting-edge research (our faculty routinely publish their results at top conferences and are recognized with distinctions such as the Sloan Research Fellowships, NSF CAREER Awards, and Best Paper Awards) and offers world-class graduate education. At the same time, TTI-Chicago faculty members enjoy a uniquely light teaching load, which helps them focus on their research. TTI-Chicago research assistant professor alumni have an excellent employment track record (https://www.ttic.edu/faculty-alumni/).
Located on the University of Chicago campus, TTI-Chicago has strong ties to the University. In addition to having access to TTI-Chicago's excellent computing infrastructure, faculty members have access to many of the University of Chicago's state-of-the-art facilities. TTI-Chicago faculty members frequently collaborate with colleagues from leading academic institutions around the world. Moreover, TTI-Chicago supports travel and visitor hosting (through annual research funds for research and tenured faculty and start-up packages for tenure-track faculty).
TTI-Chicago's faculty and students enjoy the close proximity of a vibrant urban environment with flourishing culture, business, and entertainment scenes.
We invite candidates with an outstanding academic record and passion for computer science research to join our world-class team of 12 tenured/tenure-track faculty and 11 research faculty members.
Teaching Requirements
Tenure-track faculty teach one quarter per year. Research faculty have no teaching duties, but have the opportunity to teach and co-advise students.
TTI-Chicago/Simons-Berkeley Joint Program
Applicants for research assistant professor (RAP) positions in relevant areas are encouraged to simultaneously apply for the TTI-Chicago RAP program and the Simons-Berkeley Research Fellowship. In 2020-21, the Simons Institute is running four programs: “Probability, Geometry, and Computation in High Dimensions”, “Theory of Reinforcement Learning”, “Satisfiability: Theory, Practice, and Beyond”, and “Theoretical Foundations of Computer Systems” (see http://simons.berkeley.edu/programs/current for details).
Applicants selected by TTI-Chicago will be offered an RAP position. Applicants selected by both institutions will be able to participate in a program at the Simons Institute before joining TTI-Chicago. Please note that applicants interested in the joint program must submit separate applications to TTI-Chicago and the Simons Institute.
Timeline
We will start reviewing applications on December 1, 2019, and will continue until the positions are filled.
Application Requirements
1. cover letter
2. curriculum vitae
3. research statement
4. teaching statement (optional for RAP applicants)
5. names and contact information of at least three references
If interested in the joint program, please check the Simons Fellowship requirements (https://simons.berkeley.edu/programs/fellows). Please note that the Simons Institute has a different deadline.
Where to Apply
https://ttic.edu/facultyapplication
Instead of submitting an application online, senior applicants may directly contact the Chief Academic Officer (avrim@ttic.edu) or faculty members in their areas.
Questions
recruiting@ttic.edu
TTI-Chicago is an equal opportunity employer.
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| Special CASP13 issue of Proteins has been published | (2019-11-12) |
Dear CASPers,
It is our pleasure to announce that CASP13 proceedings have been published in the December Issue of Proteins. All papers are freely accessible at:
https://onlinelibrary.wiley.com/toc/10970134/2019/87/12
Thanks to all who contributed to the issue.
CASP organizers
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| The 5th International Conference on Protein and RNA Structure Prediction, Punta Cana, Dominican Republic, Dec 2-6, 2019 | (2019-11-5) |
*** A message from the organizers of the 5th International Conference on Protein and RNA Structure Prediction ***
We still need speakers for the 5th International Conference on Protein and RNA Structure Prediction. Please consider attending this conference, and register as soon as possible. We need your support to continue organizing this conference. Everybody (including students) will have an opportunity to give a talk.
The conference registration site is:
https://ces.ucdavis.edu/confreg/index.cfm?confid=1098
The 5th International Conference on Protein and RNA Structure Prediction will be held at 5 star Riu Bambu resort. The Hotel Riu Bambu (24h All Inclusive), is situated in Punta Cana, Dominican Republic on the incredible Playa Arena Gorda beach.
The property's 5 restaurants, 6 bars/lounges, 3 poolside bars and 2 swim-up bar. Public areas and rooms are equipped with complimentary wireless Internet access.
The purpose of the 5th International Conference on Protein and RNA Structure Prediction is to bring together eminent scholars with expertise in various fields of computational modeling and prediction of structure, as well as experimentalists interested in these subjects. Since computational prediction methods continuously improve and evolve towards prediction of structure of more and more complicated biological objects our conference will cover also related topics, such prediction of structure of protein complexes, protein docking; prediction of intrinsically disordered regions in proteins, RNA structure prediction and modeling of RNA-protein assemblages. New methodologies for protein structure and function prediction will be discussed, such as physics-based approaches to the structure prediction, structural flexibility models, and development of new improved coarse-grained potentials.
A special emphasis will be given to applications of deep learning methods to structure prediction.
The list of Plenary speakers:
John Moult (University of Maryland)
Olivier Lichtarge (Baylor College of Medicine)
Andrzej Joachimiak (Argonne National Laboratory)
Ilya Vakser (University of Kansas)
Yaoqi Zhou (Griffith University)
This is a very unique possibility of meeting with Yaoqi Zhou who is one of the leaders in applying deep learning methods to protein structure prediction problems. He will travel over 30 hours each way from Australia to attend this meeting.
Invited Speakers include:
Ralf Bundschuh (The Ohio State University)
Ram Samudrala (University of Buffalo)
Daisuke Kihara (Purdue University)
Andras Fiser (Albert Einstein College of Medicine)
Lukasz Joachimiak (UT Southwestern)
Adam Sieradzan (University of Gdansk)
Uli Hansmann (University of Oklahoma)
Krzysztof Fidelis (UC Davis)
among others.
The early bird registration fee ($995 with a promo code: EARLYBIRD ) includes conference fee and all-inclusive 5 days (4 nights) hotel accommodation in a 5-star resort (including all meals & drinks and social events). It includes also free wireless internet access for the conference. You may bring your spouse for an extra charge $60 per day. Children ages 0-1 are free, children ages 1-12 sharing the room with two adults cost $50 per day per child. The registration for students who share room is $800 (the the promo code: DOUBLEROOM ).
There is a possibility of purchasing 3 extra nights before and after the conference. The cost of extra nights is $140 per night for single room and $200 for double occupancy room. Children 1-12 years old are $50 extra per night.
Please contact Andrzej Kloczkowski (Andrzej.Kloczkowski@nationwidechildrens.org) or Karen Blosser (karenblosser2012@gmail.com) with any questions.
Conference Chairs:
Andrzej Kloczkowski – Nationwide Children’s Hospital and The Ohio State University
Robert L. Jernigan – Iowa State University
Eshel Faraggi – IUPU
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| Crosslinking – assisted modeling in CASP | (2019-9-6) |
Dear CASP participants,
Sparse experimental data offer substantial added capacity for modeling difficult targets. To understand more about how the crosslinking data were used by modelers in CASP13, and to make the best use of this type of data in the upcoming CASPs, our two data providing groups have prepared a questionnaire.
We would be grateful if you could take a few minutes to answer the questions Juri Rappsilber and Alexander Leitner have prepared. You are encouraged to reply even if you have not submitted in this modeling category in previous CASPs, in this case by providing comments and recommendations at the bottom of the survey. We would definitely like to know if you plan to take part in this experiment in CASP14. You can indicate this via the survey page or by writing directly to me at kfidelis@ucdavis.edu. Questions can also be sent to Alexander or Juri – contact information is provided on the survey page.
If you have not yet done so, we strongly encourage that you consider participating in this category in CASP14!
Please find the survey at https://forms.gle/Ej9KiLTCS7PBCW9C8
The survey page will stay open until September 30, 2019.
Krzysztof Fidelis
for CASP organizers
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| Training Workshop and CAPRI Conference EBI Cambridge, 1-5 April 2019 | (2019-2-15) |
The message is sent on behalf of the conference organizers.
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CAPRI EVALUATION CONFERENCE 3-5 April 2019, EBI Hinxton, Cambridge
This meeting will be the 7th CAPRI evaluation of the community wide blind trial or predicting protein complexes. The meeting program will include an overview of the performance of protein docking and scoring procedures obtained for targets evaluated since 2016. There will be talks by the best CAPRI performers and groups developing innovative computational approaches. There will be several plenary lectures:
Madan Babu (MRC Laboratory of Molecular Biology)_
Caoline Lynn Kamerlin (Uppsala University)
Louise Walport (Crick)
Todd Yeates (UCLA)
For more details and to register go to http://www.capri-docking.org/events/
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HANDS-ON TRAINING WORSHOP 1-2 April 2019, EBI Hinxton Cambridge
A hands-on workshop sponsored by INSTRUCT-ERIC on integrative modeling of protein-protein interactions and larger multi-molecular assemblies will be held on April 1-2, two days before the CAPRI evaluation meeting.
Separate registration to this workshop is required go to http://www.capri-docking.org/events/
Topics will be:
Introduction to protein-protein docking: sampling and scoring
Practical: Flexible docking with SwarmDock
Paul A. Bates, and Raphael A.G. Chaleil, Francis Crick Institute, London, UK
Introduction to data-driven docking
Practical: Integrative docking with HADDOCK
Alexandre M.J.J. Bonvin and Panos Koukos, Bijvoet Center for Biomolecular Research, Utrecht, NL
Protein structure prediction
Practical: Modelling protein structures and variants: Phyre, PhyreRisk, Missense3D and EzMol
Michael J.E. Sternberg, Lawrence Kelley and Charles Tochukwu, Imperial College London, London, UK
The validation and verification of protein structure
Practical: Hands-on assessment of structural quality
Gerard Kleywegt, EMBL European Bioinformatics Institute, Cambridge, UK
Integrative structure determination of macromolecular assemblies
Practical: Determination of macromolecular structure using Cryo-EM data
Sony Malhotra and Maya Topf, Institute of Structural and Molecular Biology, London, UK
Protein-protein binding affinities
Practical: Modelling interaction strength using machine learning
Iain H. Moal, EMBL European Bioinformatics Institute, Cambridge, UK
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| CASP13 presentations | (2018-12-13) |
Dear CASP participants and observers,
Hope you are safely back home after a very productive and exciting meeting in Mexico. Informing you that we have posted at our website all the CASP13 presentations that were provided to us by their authors. You can find them here:
http://predictioncenter.org/casp13/doc/presentations/
CASP organizers
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| CASP13 ranking tables released | (2018-11-29) |
In accordance with the decision of CASP12 predictors' meeting, we are releasing rankings of CASP13 participants according to the formulae used by the assessors in the previous round of CASP. Ranking tables are now available from the main casp13 web page.
CASP13 rankings will be revealed at the upcoming conference and may not coincide with the ones calculated according to the CASP12 formulae.
CASP organizers
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| CASP13 program and results are available online | (2018-11-28) |
Dear CASPers,
We are sure all of you are very eager to learn your results in CASP13. The evaluation results and the program of the CASP13 conference are now available online from the http://predictioncenter.org/casp13 web page.
Interactive sortable tables and graphs are accessible by following the AUTOMATIC EVALUATION link. Target coordinates, models and evaluation tables are available also as text files through the Parseable Data link (or the Data Archive link in the website's left side Menu). Unfortunately, this CASP round, some of the target providers have been much more reluctant than usual to allow general release of target coordinates. So, at this stage we can release only coordinates of the targets, for which we explicitly received green light from their authors. We are planning to release more targets (even though not all) to active CASP participants through a password-protected gateway after the CASP13 meeting starts. A separate email will be sent to group leaders in due time.
CASP13 organizers
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| The regular registration for CASP13 is now closed; we have opened a special last minute registration | (2018-11-21) |
CASP13 this year has observed unprecedented progress in the ability of computational methods to predict protein 3D structure. The reasons are not yet fully clear, but all this, including of course the results, will be discussed at the meeting.
The regular registration for CASP13 is now closed. A special registration option now open does not include resort accommodations. Before you use this option, you should make Iberostar Paraiso Maya accommodation arrangements on your own. The Convention Center is located on the resort grounds and access is restricted to registered hotel guests. In addition to Paraiso Maya, staying at other Iberostar Paraiso hotels will also allow access to the Convention Center, but in most part not to Maya restaurants, so staying at Maya is recommended.
We would like to have you there! And we have made it possible to register at a late hour.
The airport transfer information and poster information will be posted shortly.
Meeting registration:
http://predictioncenter.org/casp13/meeting.cgi
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| Reminder: SPECIAL CASP WEBINAR - TOMORROW, October 4, 2018 | (2018-10-3) |
You are invited to a Special CASP Webinar: Protein conformational landscapes - Introduction to dynamic structural biology in CASP
Please join us via zoom (pre-download from zoom.us) by clicking on the link below at 9:30 AM (Pacific) on October 4, 2018: https://zoom.us/j/548000851.
Introduction by Guy Montelione (Rutgers) and Overview of steps in FRET-assisted modeling by Claus Seidel (Heinrich-Heine-Universitaet Duesseldorf)
More detailed information:
Proteins and protein structure are central to many aspects of biology. However, to some degree our view of protein structure is biased by our crystallographic technology -- in which we study proteins in crystal lattices. From a single crystal structure, we may sometimes get only a part of the structure-function story.
The true nature of a protein structure is an ensemble, or distribution, of structures. Sometimes this ensemble is narrow (converged), and in the limit conforms to a crystallographic picture. In other cases, it is very conformationally diverse. Consider for, example, interdomain flexibility in multidomain proteins, which may exhibit two (or more) relative orientations. Even single-domain may sample multiple conformational states. These multiple conformational states, or plasticity, often confer key functions to the protein. If we can better understand these "native-state energy landscapes", we will have a more accurate understanding of protein structures and their functions.
As a segue into the area of modeling conformational dynamics in proteins within the CASP framework, we will hold a webinar to begin to explore this paradigm using Fluorescence Resonance Energy Transfer (FRET) data. The laboratory of Prof. Claus Seidel (Heinrich-Heine-Universitaet Duesseldorf) has generated experimental FRET data for a two-domain protein (regular CASP target T0964 and FRET-assisted CASP target F0964). Preliminary analysis indicates that these two domains exhibit multiple conformational states with respect to one another. Some of the FRET probes are also located in flexible regions of the individual domains.
As a test case for modeling dynamic interdomain and intradomain motions, additional data will be released following the webinar for a second round of prediction on this target (f0964).
Claus will explain the most important steps in integrative FRET-restrained structural modeling:
(1) Efficient use of prior knowledge to create an ensemble of potential structural models
(2 )Procedure to select informative FRET pairs
(3) FRET-based measurement and analysis techniques for determining interdye distances that allow one resolve biomolecular structure and dynamics
(4) FRET-restrained structural modeling
(5) Quantitative judgement of the structural models with respect to their precision and accuracy
Please contact Krzysztof Fidelis kfidelis@ucdavis.edu with any questions regarding this webinar.
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| SPECIAL CASP WEBINAR - October 4, 2018 | (2018-9-28) |
You are invited to a Special CASP Webinar: Protein conformational landscapes - Introduction to dynamic structural biology in CASP
Please join us via zoom (pre-download from zoom.us) by clicking on the link below at 9:30 AM (Pacific) on October 4, 2018: https://zoom.us/j/548000851.
Introduction by Guy Montelione (Rutgers) and Overview of steps in FRET-assisted modeling by Claus Seidel (Heinrich-Heine-Universitaet Duesseldorf)
More detailed information:
Proteins and protein structure are central to many aspects of biology. However, to some degree our view of protein structure is biased by our crystallographic technology -- in which we study proteins in crystal lattices. From a single crystal structure, we may sometimes get only a part of the structure-function story.
The true nature of a protein structure is an ensemble, or distribution, of structures. Sometimes this ensemble is narrow (converged), and in the limit conforms to a crystallographic picture. In other cases, it is very conformationally diverse. Consider for, example, interdomain flexibility in multidomain proteins, which may exhibit two (or more) relative orientations. Even single-domain may sample multiple conformational states. These multiple conformational states, or plasticity, often confer key functions to the protein. If we can better understand these "native-state energy landscapes", we will have a more accurate understanding of protein structures and their functions.
As a segue into the area of modeling conformational dynamics in proteins within the CASP framework, we will hold a webinar to begin to explore this paradigm using Fluorescence Resonance Energy Transfer (FRET) data. The laboratory of Prof. Claus Seidel (Heinrich-Heine-Universitaet Duesseldorf) has generated experimental FRET data for a two-domain protein (regular CASP target T0964 and FRET-assisted CASP target F0964). Preliminary analysis indicates that these two domains exhibit multiple conformational states with respect to one another. Some of the FRET probes are also located in flexible regions of the individual domains.
As a test case for modeling dynamic interdomain and intradomain motions, additional data will be released following the webinar for a second round of prediction on this target (f0964).
Claus will explain the most important steps in integrative FRET-restrained structural modeling:
(1) Efficient use of prior knowledge to create an ensemble of potential structural models
(2 )Procedure to select informative FRET pairs
(3) FRET-based measurement and analysis techniques for determining interdye distances that allow one resolve biomolecular structure and dynamics
(4) FRET-restrained structural modeling
(5) Quantitative judgement of the structural models with respect to their precision and accuracy
Please contact Krzysztof Fidelis kfidelis@ucdavis.edu with any questions regarding this webinar.
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| Second stage of NMR-assisted data for target T1008; abstracts are due this Saturday | (2018-9-18) |
Dear predictors,
Two messages for you.
1. We announced earlier that real NMR-assisted data from target T1008 will be released in two stages. The first stage prediction has been closed last week. Today we are releasing the second stage data (target n1008, starting from the lowercase 'n'). With respect to the first stage target N1008, now both backbone AND extensive sidechain resonance assignments were used to generate the Ambiguous Contact file, so the false positive rate is very low. There is also a README explaining the data.
2. Only 4 days are left for submitting your CASP13 methods abstracts. Please remember that, as usually, your contributions will be taken into account in choosing presentations for the meeting.
CASP13 organizers
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| Symposium on Computational Structural Biology celebrating 25 years of SWISS-MODEL: October 18, 2018, in Basel | (2018-9-11) |
Dear colleagues,
Join us on 18 October 2018 in Basel for a symposium on Computational Structural Biology celebrating 25 years of SWISS-MODEL.
Confirmed speakers include:
John Moult, University of Maryland, Washington, USA
Christine Orengo, University College London, London UK
Chaok Seok, Seol University, Seol, ROK
Janet Thornton, European Bioinformatics Institute, Hinxton, UK
Manuel Peitsch, Founder of SWISS-MODEL, PMI, Neuchâtel, CH
Call for abstract and registration are open at: https://swissmodel.expasy.org/25years/
Looking forward to welcoming you in Basel,
Rosalba Lepore & Torsten Schwede
«SWISS-MODEL 25 Years Symposium» Program Chairs
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The SWISS-MODEL 25 Years Symposium is organized in collaboration with the SIB Swiss Institute of Bioinformatics & Biozentrum University of Basel, and takes place on 18th October 2018 at the Congress Center Basel, Messeplatz 21, CH-4058 Basel. For more information, please visit https://swissmodel.expasy.org/25years.
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| CASP13 Mexico Meeting Early Bird rates will remain in effect until September 17 | (2018-9-6) |
Dear CASP Participants and Friends,
Writing to those of you who have not yet registered for the December Meeting in Mexico – the Early Bird rates will remain in effect until September 17, 2018 ($1,400/1,200 single/shared occupancy rate includes the meeting registration fee, lodging, and meals for the duration of the conference).
CASP13 featured 90 protein targets. Over 57,000 predictions were submitted, including close to 36,000 tertiary structure models, 3,000 oligomeric models, 2,000 data-assisted models, 4,000 sets of contact predictions, 4,000 refined models, and 9,000 sets of accuracy estimations.
The conference will feature assessment talks, reports from the best predictors, and keynote presentations. The keynote speakers represent two current areas of special interest in CASP, machine learning /deep learning in structural biology and cryo-EM driven modeling:
* David Koes (U Pittsburgh), is a pioneer in the application of convolutional neural networks to molecular docking
* Wah Chiu (Stanford), is a leader in cryo-electron microscopy.
CASP13 will be held December 1-4, 2018, at the Iberostar Paraiso Maya resort (site of the CASP11 conference in 2014, destination airport is Cancun - CUN). Accompanying person fee is $330 for the duration of the conference. The agreement with the hotel extends registration at the conference rates to 3 days before and after the meeting.
Please share this information with your colleagues. The meeting poster is available at the conference registration site: http://predictioncenter.org/casp13/meeting.cgi
CASP organizers
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| Please send in your CASP13 methods abstracts | (2018-8-31) |
Dear predictors,
We have opened the webpage for collecting methods abstracts. The deadline for submitting the abstracts is September 22, 2018. Please read the instructions carefully and address all the questions specified in the Abstract submission form (http://predictioncenter.org/casp13/abstracts.cgi). Please remember that, as usually, your contributions will be taken into account in choosing presentations for the meeting.
CASP organizers
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| A message from the ogranizers of MPI 2018 | (2018-8-30) |
We apologize if this announcement reaches you more than once…
MPI 2018 - MODELING OF PROTEIN INTERACTIONS
November 8 - 10, 2018, Lawrence, KS
http://conferences.compbio.ku.edu/mpi2018
CALL FOR PAPERS
The MPI conference (Charleston 2001, Stony Brook 2003, Lawrence 2005 - 2018 http://conferences.compbio.ku.edu/) plays an important role in the biomolecular modeling community, discussing current progress and setting new goals in this rapidly evolving field. As in the previous meetings, we intend to keep the focus on theoretical foundations of the field and its interface with the experimental studies.
ORGANIZERS
Ilya Vakser, The University of Kansas
Sandor Vajda, Boston University
PROGRAM
MULTISCALE MODELING, DOCKING, FOLDING, BINDING, FUNCTION, DESIGN OF PROTEIN INTERFACES, INHIBITION OF PPI, AND MORE...
SPEAKERS
For the current list of our Invited Speakers see http://conferences.compbio.ku.edu/mpi2018/speakers.php
LOCATION
The meeting will take place at The Eldridge hotel in downtown Lawrence, KS. The Eldridge is a historic hotel in the heart of a college town with art galleries, boutique shopping, outdoor dining and live music.
PARTICIPATION
The number of participants is limited. In selecting participants, the preference will be given to those who would present a poster on the subject of the conference. If you would like to attend the conference, please submit a request as soon as possible by e-mail to Ilya Vakser (vakser@ku.edu) or Sandor Vajda (vajda@bu.edu). Include a brief (a few sentences) description of your research, your full affiliation, and position (faculty, postdoc, student, etc.). If you would like to present a poster, please include a half-page abstract. If your application is accepted, we will send you information needed for registration. The early registration fee for the participants of the conference is $390 ($290 for postdocs and students). After October 5, the fee will be $450 ($350 for postdocs and students).
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| Clarification on the N0980 data set from the data providers | (2018-8-21) |
In the case of data-assisted target N0980, the crystal structure is a homodimer of heterodimers. Each heterodimer consists of two subunits (e.g. A and B for one heterodimer, C and D for the other heterodimer).
For simulated NMR data in CASP13, we did not attempt to deal with the special cases of ambiguity that arise in homodimers. NMR studies of homodimers (or homodimers of heterodimers) use specialized NMR experiments and samples (i.e. X-filtered NOESY data), which we decided not to simulate for CASP13 [we do plan, however, to add these cases in future CASP experiments using both simulated and real NMR data].
Therefore, for CASP13 target N0980, the target structure for assessment is the A-B heterodimer (i.e. we assumed the dimer of heterodimers is dissociated in solution into the corresponding heterodimers, for which NMR data were generated). From the perspective of NMR, such a heterodimer is essentially like a single-chain protein with a break along the chain.
We also generated a separate NMR data set for the first subunit of target H0980. These data constitute a separate data-assisted target N0980s1.
Gaetano Montelione,
CASP13 NMR-assisted assessor
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| REMINDER: Early bird registration ends shortly | (2018-8-14) |
We are gathering at a beautiful resort on Riviera Maya, come and join us!
* Analyze the fascinating results of CASP13
* Discuss the newest advancements in the field
* Develop collaborations
* Explore the job market
CASP13 will be held Dec. 1-4, 2018, at the Iberostar Paraiso Maya resort (site of the CASP11 in 2014,
destination airport is Cancun - CUN).
The Early Bird prices will remain available until August 17 so please register promptly. Accompanying person fee is
$330 for the duration of the conference. The agreement with the hotel extends registration at the conference rates
to 3 days before and after the meeting. If you plan to come with children under 13, please contact us for special arrangements (children under 3 stay free).
Please share this information with your colleagues. The meeting poster is available at the conference registration
site: http://predictioncenter.org/casp13/meeting.cgi
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| End of target release in CASP13 | (2018-8-10) |
Today we have finished releasing targets in CASP13. All in all, we released 90 regular targets; 13 hetero-multimer targets; 31 refinement targets; and 49 assisted modeling prediction targets in 5 data-assisted categories - SAXS, XL-MS, NMR (simulated and real data), SANS and FRET.
This past week we had quite an intense schedule for releasing refinement and data-assisted targets: 9 new refinement targets; 2 XL-MS targets; 9 NMR -assisted targets (8 simulated datasets and 1 real dataset); and 1 FRET data-assisted modeling target (F0964).
FRET data type is new in CASP. Similarly to SANS-assisted results, the FRET-assisted results will not be competitively assessed in CASP13. Rather, with this target we are initiating a discussion and allowing for a learning experience with the development of future FRET-based modeling techniques in mind. We are providing ample time to model this target with the closing date of September 30 (pending approval from the structure's author). The molecule’s two domains seem open to homology modeling but the relative domain orientation is not known (we have the structure of only the second of the two domains starting with the residues VIVIGDE). The FRET data suggest that there may be a distribution of domain orientations, opening a challenge of dynamic modeling in CASP. This topic will be discussed at the CASP13 meeting.
The description of the FRET data and an overview of the results for target F0964 can be found at http://predictioncenter.org/casp13/doc/FRET_CASP13_AGSeidel.pdf.
The detailed FRET data will be released progressively as they become available.
CASP organizers
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| Updated NMR simulated data package for N0980s1 | (2018-8-8) |
Dear NMR-assisted predictors,
Please note that we have updated the data package for target N0980s1 (released yesterday). An older package was replaced with the new one at http://predictioncenter.org/download_area/CASP13/extra_experiments/
CASP organizers
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| End of regular prediction season; last week of releasing special interest targets | (2018-8-6) |
Today (Monday, August 6) we have accepted the last regular prediction in CASP13. Thanks to all 182 prediction groups who participated in the main-stream CASP13 experiment and submitted over 50,000 models ! You deserve now a good rest after a busy, but (we hope) an exciting summer!
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The predictions season is still continuing for the refinement and data-assisted predictors. This week we are releasing the final batch of refinement and data-assisted targets. We plan to release
* the last cross-linking target (tomorrow, August 7)
* 6-7 more refinement targets
* 9 NMR-assisted targets
Unfortunately, we had to cancel one NMR-assisted target (N0953s2) due to the structure release last Wednesday.
CASP organizers
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| CASP13 is back to normal operation | (2018-7-30) |
Dear CASPers,
After the recent crash, we delegated responsibilities of the main CASP13 web server to yet another machine. We hope that all services in CASP13 are back, but if you notice any problems - please let us know. We are planning to keep this machine as the main CASP server only temporary (till the end of the prediction season) and then migrate to a (hopefully) more reliable system.
Now when the web site is fixed, we are arranging for accommodating models of the targets that have expired during the crash. We have just updated the deadlines for all the targets that were scheduled to expire on July 27-30 ([TH]1011-1018, R0986s1, R0986s2, R0977-D2) to August 1. If you missed any of the deadlines for these targets you can (re)submit your models now. Please check your prediction pages (http://www.predictioncenter.org/casp13/predictions.cgi) to make sure that all your Friday-Monday predictions are in. It is possible that some of the predictions that were submitted on Friday, July 27, and have been accepted by our system are not visible through your prediction pages any more. This is because our database backups are done nightly, so the predictions that were sent on Friday morning PDT have not made it to the backup, from which we recreated all the CASP13 data. We do have files for those 'missing' predictions on our hard drives (the file backups are done hourly) and are planning to push those predictions through the system in the next couple of days. To make sure that your Friday-submitted predictions are in the system, we suggest you to either resubmit them by the August 1 deadline yourself or recheck your prediction pages on August 3, when we are planning to finish pushing the missing prediction files through the system.
As always, if you have any problems or questions - please send them to casp@predictioncenter.org (should work now!) or to your favorite organizer.
We apologize for all the inconveniences the hardware failure has caused, but these are the things that we could not easily control. And finally, thanks for all the messages of support and appreciation during this very stressful period for the Prediction Center team. Much appreciated!
CASP organizers
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| Main CASP server is down - please send your models to the backup server | (2018-7-27) |
Dear predictors,
It is another Friday night and another hardware failure at the Prediction Center. This time we lost the motherboard and hard disks on the main server (around 16:30 PDT). Before our system administrators switch Internet traffic to the old DNS name http://predictioncenter.org (which likely will not happen before Monday), we ask you to use the backup server's DNS http://predictioncenter5.genomecenter.ucdavis.edu for all model submissions. The web Prediction Submission Form (http://predictioncenter5.genomecenter.ucdavis.edu/casp13/predictions_submission.cgi) should work as usual. Submission through the email is temporary unavailable. If you or your server submit predictions by email, please wait with your submissions until Monday (we will extend deadlines for the expired targets).
Sorry for the inconvenience.
CASP organizers
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| Job posting; Additional info on some cross-linking datasets | (2018-7-18) |
New 'Job postings in the field' category on the FORCASP forum:
We have started a new section on the FORCASP forum dedicated to job announcements in the research /teaching areas related to CASP. We start with the announcement from the Montelione and Nanda groups at Rutgers in the area of computational NMR (www.forcasp.org).
Additional information on some cross-linking datasets:
This is now available for the small-'x' targets in the Description column of the Target list and in the Additional Information section of target-specific pages (e.g., http://predictioncenter.org/casp13/target.cgi?id=153&view=all).
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| End of the regular target release; plans for refinement and data-assisted targets | (2018-7-17) |
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Regular targets:
Today (July 17) we released the last regular CASP13 target. All in all, we released 90 tertiary structure prediction targets, quite a representative data set ! The CASP13 target set differs from those of previous CASPs in several aspects. First, we had more than ever hetero-complex targets - 13. Second, we had many more large targets: 22 targets longer than 500 residues in CASP13 compared to 6 or less in five previous CASPs. Third, we had 8 targets (13 different subunits) solved with the cryo-EM technique, compared to 3 subunits in CASP12 and none before that. Finally, we had many more targets for assembly prediction, what also resulted in more targets for CAPRI (20 total in CASP13).
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Refinement targets:
We will continue releasing refinement targets throughout the next 3 weeks. This week we will release three targets, one per day on Wed, Thu and Fri.
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Data-assisted targets:
SAXS-assisted: we have released all SAXS-assisted targets (11 data sets resulting in 17 targets). Thanks to Greg Hura and Susan Tsutakawa (J.Tainer's group, LBL) for preparing experimental data on these targets.
SANS-assisted: we have released all SANS-assisted targets (1). Thanks to Anne Martel and Sergei Grudinin for preparing the data.
X-linking- assisted: we have released 5 XL-MS data sets (Alexander Leitner's group) and 2 XL-MS data sets (Juri Rappsilber's group) resulting in 17 targets. Three more data sets from A. Leitner's group will be released between now and July 30. More data sets from J. Rappsilber's group are possible.
NMR-simulated and real NMR-assisted: over the next 3 weeks, we will release contacts derived from NMR spectra that have been simulated for several FM targets (Gaetano Montelione's group). In addition, a real NMR data set has been generated for one CASP target, and a second real NMR data set for another protein is anticipated. Predictors may use these NMR data, together with contact predictions (ECs), crosslink data, and/or SAXS data, for data-guided structure prediction. A description of these sparse NMR data will be provided with the data. The first target is expected the coming Friday, July 20.
CASP organizers
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| CASP13 meeting registration | (2018-7-13) |
We are gathering at a beautiful resort on Riviera Maya, come and join us!
* Analyze the fascinating results of CASP13
* Discuss the newest advancements in the field
* Develop collaborations
* Explore the job market
CASP13 will be held Dec. 1-4, 2018, at the Iberostar Paraiso Maya resort (site of the CASP11 in 2014, destination airport is Cancun - CUN).
The registration is now open. We are able to hold the Early Bird prices until August 17 so please register promptly. Accompanying person fee is $330 for the duration of the conference. The agreement with the hotel extends registration at the conference rates to 3 days before and after the meeting. If you plan to come with children under 13, please contact us for special arrangements (children under 3 stay free).
Please share this information with your colleagues. The meeting poster is available at the conference registration site: http://predictioncenter.org/casp13/meeting.cgi
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| Week of July 16: wrapping up the regular target release | (2018-7-12) |
This week we were able to secure 3 very interesting cryo-EM targets. To accommodate them all in CASP, we will need one more day beyond what was originally planned. The targets will be released one per day, tomorrow, next Monday and next Tuesday, July 17. This will conclude the CASP13 regular target release season!
We received a request not to shorten prediction period for the last targets, so that enough time is allotted for their prediction. To accommodate it, we will set prediction deadlines for the last three targets in the first week of August.
CASP organizers
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| Week 11 (July 9-13) | (2018-7-6) |
Target release plan for July 9-13:
Next week is the last full week of target release in CASP13. We plan to go with 2 new targets per day Monday through Friday, including 3 heterocomplexes on Tue-Thu. We would also have 1 SAXS -assisted target (most likely the last SAXS -assisted target this season), 2+ refinement targets, and 1 cross-linking target (depending on the experimental data availability).
Week of July 16:
According to the announced CASP13 timetable, July 16 was planned as the last day for releasing regular targets. As of today, we do not have any targets for that day, but we do have a couple of good leads that may result in a few targets. If we get more targets than we can fit in a one-day release, we may extend the target release season by one or two days in order to accommodate those targets in CASP13. We will announce the final plans not later than Thursday of the next week.
Refinement and data-assisted targets:
We will continue releasing refinement and data-assisted targets through the first week of August.
Meeting registration:
We are planning to open registration for CASP13 conference next week.
Summary for the first 10 weeks of CASP:
* 71 tertiary structure prediction targets
* 7 heteromer targets
* 12 refinement targets
* 10 SAXS data sets resulting in 16 prediction targets
* 3+1 XL-MS data sets resulting in 12 prediction targets
* ~35,000 predictions from 179 groups
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| Week 10 (July 2-6) | (2018-6-29) |
Next week will be the second to last in a typical 11-week CASP target release season. We plan to release:
* 6 regular targets (no targets on Wednesday)
* 2 SAXS -assisted targets (Tue and Fri)
* 1 XL-MS -assisted target (same target H0957, different X-linking data acquisition technique - please comment in REMARKS on the use of a particular XLMS data set(s) )
* 5-6 refinement targets
* 1 CAPRI target
* 1 SANS -assisted target (a pilot, non-competitive trial)
* 2 simulated NMR data-assisted targets
T0988: canceled
It has been brought to our attention that target T0988 has virtually identical sequence to a previous CASP12 target T0881, and therefore we are canceling it.
Summary for the first 9 weeks of CASP:
* 64 tertiary structure prediction targets
* 7 heteromer targets
* 8 refinement targets
* 8 SAXS data sets resulting in 16 prediction targets
* 3 XL-MS data sets resulting in 9 prediction targets
* >30,000 predictions from 179 groups
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| Your participation in data assisted modeling | (2018-6-28) |
Current CASP offers notably interesting targets in the data assisted category. We are working with two cross-linking mass spectrometry groups and a group providing SAXS data. In addition, we will provide SANS and possibly FRET data in an exploratory mode, this time mostly as an illustration of what is possible with these two techniques.
In particular, we would like to direct your attention to protein complexes, where additional cross-linking and SAXS data maybe a make-it-or-break-it factor in successful modeling of these targets (e.g. CASP targets 953, 957, and 968, possibly more to come - stay tuned).
CASP organizers
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| Week 9 (June 25-29) | (2018-6-22) |
Target release plans for week 9:
* 6 regular targets, including one longer target on Mon, Wed-Fri, and two shorter targets on Tuesday
* 2 SAXS-assisted targets
* 1 XL-MS -assisted target
* some refinement targets (depending on the evaluation results)
* no CAPRI targets
Please note that the next week we are starting second thousand of regular CASP targets. A request to server predictors: please make sure your scripts can process regular targets with the second symbol in the target name not being 0 any more (e.g., T1000).
Summary for the first 8 weeks of CASP:
* 58 tertiary structure prediction targets
* 7 heteromer targets
* 8 refinement targets
* 5 SAXS data sets resulting in 13 prediction targets
* 2 XL-MS data sets resulting in 6 prediction targets
* >26,000 predictions from 178 groups
CASP organizers
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| Week 8 (June 18-22) | (2018-6-15) |
Target release plans for week 8:
* 6 regular targets, including 3 targets larger than 500 residues
* 1 SAXS-assisted target (Friday)
* some refinement targets (depending on the evaluation results)
* 2 or 3 CAPRI targets
Data-assisted targets:
This week we released first two cross-linking assisted targets - H0953 and H0957. More to follow in the last week of June.
In addition to the four already released SAXS-assisted targets, we are expecting at least five more later in the prediction season.
First sparse NMR data-assisted targets are expected in the end of this month.
T0999 (Friday):
Next week we are scheduled to reach another milestone in the CASP history: Friday will mark the last target from the first thousand of CASP targets overall. And it will be a special target! T0999 will be the largest target ever released in CASP. It is a homodimer of ~3200 residues total (~1600 residues in each chain). Predictors should be able to easily find that each chain of this target is a fusion of 5 enzymes. Even though prediction of individual domains is not expected to be very challenging (all five domains have multiple good templates), the arrangement of 10 domains within the complex is unknown and may be rather a difficult task! To make the story even more interesting, we have the SAXS and cross-linking data for this target, and planning to release those in turn after the regular prediction is over. It would be interesting to see if these data help generate better quaternary structure for such a large target.
Summary for the first 7 weeks of CASP:
* 52 tertiary structure prediction targets
* 7 heteromer targets
* 7 refinement targets
* 4 SAXS data sets resulting in 10 prediction targets
* 2 XL-MS data sets resulting in 6 prediction targets
* >22,000 predictions from 173 groups
CASP organizers
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| Week 7 (June 11-15) | (2018-6-8) |
Target release plans for week 7:
* 8 regular targets
* 1 heteromeric target (Fri)
* 1 SAXS-assisted target
* 2 XL-MS assisted targets
* ? refinement targets
* 2 CAPRI targets (Tue, Fri)
T0970:
Analyzing structure of T0970 we noticed that the original sequence was provided to CASP with trimmed off disorder regions. The correct sequence is:
KRSGFLTLGYRGSY[TTVRDNQADAKFRR]VARIMVCGRIALAKEVFGDTLNESRD[PDRQP]EKYTSRFYLKFTYLEQAFDRLSEAGFHMVACNSSGTAAF[VNQ]YRDDKIWSSYTEYIFFRP
(three disordered regions are provided in brackets).
Even though the absence of disorder residues in models will not affect the evaluation (we would cut them off for evaluation purposes anyways), we do realize that not knowing about the presence of these residues in the protein sequence might distort the modeling procedure as prediction methods could try to connect residues Y14 and V15 in the provided sequence by a peptide bond, while in fact these residues are 14 residues apart in the complete protein sequence. Please check your predictions and adjust structures if needed for this sequence mistake (please continue using residue numbering from the originally released sequence).
Contact predictions for long targets:
CASP system allows accepting predictions up to 300,000 lines in a file. For long targets, this may not be enough to submit the whole contact map. However, in practice submitting the whole contact map is rarely needed.
First, you can eliminate pairs of residues separated by fewer than 12 positions as short-range contacts have never been assessed in CASP contact prediction. Next, you don't need to include contact pairs predicted with close to zero probability as missing pairs are assumed to be predicted with 0 probability anyways. Following these two advises can substantially reduce your file size. If you nevertheless think that the whole contact map may be beneficial for evaluation, please submit the reduced prediction through the CASP gateway and, in addition to this, write to us and we would instruct you where to upload your complete contact map file.
Summary for the first 6 weeks of CASP:
* 44 tertiary structure prediction targets
* 6 heteromer targets
* 4 refinement targets
* 3 SAXS-assisted prediction targets (7 with subunits)
* 18,000 predictions from 166 groups
CASP organizers
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| Refinement target R0958 canceled | (2018-6-4) |
Dear refinement predictors,
We are forced to cancel target R0958 as a manuscript describing its structure became available online.
CASP organizers
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| Question and answer session for CASP participants | (2018-6-1) |
We are wondering if any CASP participants would like us to organize a "Data Guided Prediction" question and answer session with the people providing SAXS, Cross-link, and/or NMR data. Please respond to casp@predictioncenter.org so we have an idea of how much need there is for such a Q&A session.
CASP organizers and data providers
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| Plans for week 6 (June 4-8) | (2018-6-1) |
Target release:
* 7 regular targets, including 2 CAPRI (Tue, Wed)
Warning. Server groups should be prepared for processing large targets on Wednesday (target T0984, ~750 res.) and Thursday (target T0985, 850 res.)
* 1 heteromeric target (Fri)
* 2+ refinement targets
H0968:
The original stoichiometry for this target was suggested as A1B1. The assembly assessors think that higher-agglomeration arrangement is also feasible, so we are changing the suggested stoichiometry from A1B1 to A2B2 so that those wishing to send us models as an A2B2 complex could do that.
Summary for the first 5 weeks of CASP:
* 37 tertiary structure prediction targets
* 5 heteromer targets
* 2 refinement targets
* 3 assisted prediction targets (7 with subunits)
* 14,000 predictions from 164 groups
CASP organizers
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| T0960 and T0963 | (2018-5-30) |
Dear predictors,
It was brought to our attention that a good picture (not coordinates) for targets T0960 and T0963 is available in a published doctoral thesis, see page 27:
https://infoscience.epfl.ch/record/196246/files/EPFL_TH5939.pdf .
In order not to cancel two interesting targets, we will be evaluating server predictions on these targets as we typically do for server-only targets. In addition to this, we would also suggest assessors to separately evaluate human predictions as a special 'assisted modeling' case. To give you some more time for the 'assisted' modeling of target T0960, which was scheduled to expire tomorrow, we extend the prediction window for this target till June 5.
CASP organizers
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| Plans for week 5 (May 28 - June 1) | (2018-5-25) |
There will be no targets on Monday.
Tuesday through Friday we will release:
* 7 regular targets, including 1 CAPRI
* 1 heteromeric target (Friday)
* 2 SAXS-assisted targets
* at least 1 refinement target
CASP organizers
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| Reminder - Thursday WEBINAR (Cross-linking) | (2018-5-23) |
Dear CASP Predictors,
This is a reminder about the introductory webinar for the Cross-linking data assisted predictions.
Speakers: Alexander Leitner and Esben Trabjerg, ETH, Zurich.
Time: 8:00 AM Pacific, 11:00 AM Eastern, 5:00 PM in Europe, late night in India, China, Japan, and Korea.
We recommend you have the Zoom application installed on your computer or mobile device (https://zoom.us). Please join by using the following link:
https://zoom.us/j/501695229
(We will open several minutes ahead of time).
CASP organizers and data providers
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| Cross-linking tutorial this Thursday | (2018-5-22) |
Dear CASP Predictors,
We are going to hold a webinar for the cross-linking assisted category. Only one session will be held, and you are invited to join via Zoom this Thursday, May 24, at 8:00 AM Pacific, 11:00 AM Eastern, 5:00 PM in Europe, late night in China, Japan, and Korea. The speakers will be Alexander Leitner and Esben Trabjerg from ETH, Zurich, providing information targeted at understanding the data and ways that the data can be integrated into algorithms. We will be recording the tutorial and making it publicly available through the Prediction Center website.
To participate, you will need to have Zoom application installed on your computer or mobile device (sign-up for free at https://zoom.us). Once installed, you should be able to join the webinar by clicking on the link https://zoom.us/j/501695229 five minutes before the start of the session.
CASP organizers and data providers
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| Reclassifying T0959 as an all-group target | (2018-5-22) |
Preliminary evaluation of server predictions submitted on target T0959 showed that the target was more difficult for prediction than originally expected. Therefore, we are reclassifying this target to 'all-group' targets and inviting human groups to submit predictions within the next two weeks (submission deadline - June 5).
CASP organizers
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| A link to the published structure of T0952 | (2018-5-5) |
Yesterday we announced that we canceled target T0952 due to the premature release of structural information. Several predictors requested a link to the paper to check their already constructed predictions. Here it comes: https://doi.org/10.1002/1873-3468.13060.
CASP organizers
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| Week 2 plans | (2018-5-4) |
We are ending the first week of CASP13 prediction season with six single-unit targets, one hetero-complex target and 54 groups submitting predictions (including 47 servers). On Sunday we will be automatically sending the first queries to the registered QA servers. Unfortunately, we already have to cancel one target - T0952, as a paper describing the structure was posted online sooner as it was expected by the structure's authors and the organizers.
Next week we will release one target on Monday and Friday, two on Tuesday and Thursday, and a heterocomplex with subunits on Wednesday. Submitted server models for the first CASP13 target, T0949, will be made available through our website on Tuesday, May 8.
CASP organizers
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| CASP13 starts tomorrow, May 1, 2018 | (2018-4-30) |
We are set to start the 13th CASP prediction season. As of today, more than 160 groups have registered, including 80 servers. Dry runs for servers are now over, and if you did not manage to test your server during those runs we will do our best to help you in the first days of CASP13. If you are planning to participate (either as a human expert group or a server group), but have not registered yet - please do this as soon as possible.
We will start CASP13 tomorrow with one relatively easy for modeling target, T0949.
On Wednesday, we will release a 'burning' target, T0950. Crystallographers who solved this target want to make it publicly available without any delays and expect the structure to be released by the PDB in the closest week or two. This is a difficult modeling target and we don't want to loose it for CASP. Therefore, this target will be released for prediction with a shorter 2-week deadline. If we learn that the prediction window for this target can be extended (or vise versa need to be further shortened) we will inform you immediately. If you participate as an expert group - please make this target your first week priority.
Two more targets, a server-only target and a human target representing short dimerization domain, will be released on Thursday.
On Friday we will suggest for modeling a difficult heteromeric structure (A3B1 stoichiometry), which will be released as 3 separate targets: a full complex target H0953, and two constitutive subunits (T0953s1 and T0953s2). For those submitting models for the whole complex there is no need to additionally send models on subunit targets (please see our format page for details http://predictioncenter.org/casp13/index.cgi?page=format#TS).
Good luck!
CASP organizers
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| Dry run continues for all types of servers | (2018-4-24) |
We have finished the first round of checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. We sent at least one test target to all registered servers, to some - two. If you had registered a TS or RR server, but have not received at least one request from us please check the Server Queries link from the main CASP13 web page to see the status of the queries to your server. In case you notice any problems, please check your registration settings and contact us if in doubt. Also, if you do not see your prediction(s) as accepted in our server status page (link Server Prediction Status) or through the Model Viewer /My CASP13 Profile pages, then either your prediction did not reach us or was rejected due to unregistered with CASP submission email or format issues.
Today we also started testing accuracy estimate servers (QA), which were sent a stage one query to estimate accuracy of 20 test models. A stage 2 query to QA servers will be sent in the due time (Wednesday, around noon PDT).
A request to EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T1111 - query received by MY_SERVER". Failing to do this may affect the timely addressing of unexpected connectivity failures.
We have one more week to help bring your servers in contact with our distribution server and make sure your submission format is correct. The first CASP13 target will be released as planned, on May 1.
CASP organizers
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| Reminder - Monday WEBINARS (data assisted category) | (2018-4-21) |
Dear CASP Predictors,
This is a reminder about the introductory webinars in the data-assisted category.
Speakers: Gaetano Montelione (NMR); Susan Tsutakawa and Greg Hura (SAXS); question and answer session
Time: 8AM Pacific and 5PM Pacific (Monday, April 23, two equivalent sessions)
Webinar will be recorded and posted on the CASP website. Slides from the talks will also be provided.
The webinars are expected to last approximately 1.5 hours.
If at all possible, please enter your name, email address, and institution upon Zoom login - this will help us communicate better in the future.
We recommend you have the Zoom application installed on your computer or mobile device (https://zoom.us). Please join by using the following link:
https://lbnl.zoom.us/j/709342869
(We will open several minutes ahead of time).
CASP organizers and data providers
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| Contacts helping 3D prediction | (2018-4-18) |
Dear prospective CASP13 participants,
The most notable progress in the recent two CASPs resulted from sustained improvement in methods for predicting three-dimensional contacts between pairs of residues in structures. Theoretical advance in contact prediction led to improved accuracy of 3D models, especially for the hardest template-free modeling cases. This progress is well documented in the latest CASP assessments of free modeling and contact prediction. However, it was difficult for the assessors to clearly quantify influence of novel contact prediction techniques on accuracy of 3D models based on the CASP data exclusively, as the assessors oftentimes did not have baseline results obtained without the contacts. To address the issue, the assessors had to perform a-posteriori modeling themselves or ask methods developers help them in staging additional tests. This could be avoided had we had 3D predictions obtained separately with and without using novel contact prediction techniques. Therefore, for CASP13 we have a following request. If you can easily disentangle the contact prediction module form the rest of your 3D-structure prediction package, we would appreciate if in addition to registering your most advanced modeling pipeline you also register a separate structure prediction method capable of generating coordinates without using advanced contact prediction methods. Please drop us a message if you can do that so that we could increase the number of allowed CASP13 groups for you.
Thank you.
CASP organizers
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| Webinars on NMR-assisted and SAXS-assisted data - April 23, 2018 | (2018-4-17) |
For the SAXS and NMR data-assisted category, we are holding webinars for the structure prediction community who wish to learn more. Data providers - Greg Hura and Susan Tsutakawa (SAXS), and Gaetano Montelione (NMR) will give targeted information at understanding the data and ways that the data can be integrated into algorithms. We will be doing two similar tutorials (8 am and 5 pm Pacific Time on April 23rd), one of which will hopefully overlap with your time zone. We will also be recording one of the tutorials and making it publicly available. The basic outline of the sessions will be: SAXS - theory, data provided, strategies for best use of data; NMR - theory, data provided, strategies for best use of data; logistics for when the data-assisted category will be open for download; questions from predictors.
To participate, you would need to have Zoom application installed on your computer or mobile device (sign-up for free at https://zoom.us). Once installed, you should be able to join the webinar by clicking on the link https://lbnl.zoom.us/j/709342869 five minutes before the start of the session.
CASP organizers and the data providers
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| CASP13 dry run for servers | (2018-4-17) |
Registration for CASP13 is currently under way, and as of now we have already a healthy participation with 98 research groups (including 43 servers) registered. We are starting checking connectivity and correctness of prediction format for the servers in the TS categories (tertiary structure and assembly) and RR category tomorrow, April 18. Testing model accuracy servers (QA) will start next Monday, April 23. If you plan to participate in the server track of CASP13 but have not registered your server(s) yet - we advise you to do so ASAP. We will be sending your servers a request to predict a test target, which, obviously, will not be a part of the CASP13 experiment. The target will be a heteromer if your server is signed for assembly prediction, or a monomer otherwise. Please consult our format page (http://predictioncenter.org/casp13/index.cgi?page=format) for prediction format details.
CASP organizers
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| End of CASP_Commons | (2018-4-17) |
Dear CASP_Commons participants,
We have finished collecting models on the 32 community-nominated targets. Thanks to everyone who participated!
The Prediction Center now will run accuracy evaluation tools on these models, package them and send to the structural biologists who suggested the targets. We will request feedback on the utility of the submitted models. In case the biologists find the models useful, we will get them in touch with you to further extend the collaboration. Stay tuned.
CASP organizers
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| CASP13 registration is open | (2018-4-4) |
Dear CASP participants,
A new, thirteenth CASP prediction season starts on May 1, 2018, and the organizers (and we are sure the majority of you too) are eager to see where the field stands after the latest quite interesting and eventful CASP12 experiment.
The registration for CASP13 has just opened. Please go to our CASP13 web page (http://predictioncenter.org/casp13), and register for the prediction challenge. Please read the description of the experiment and familiarize yourself with the format requirements, as some of them have changed. If you have questions /comments about the upcoming experiment - please let us know by replying to this message or posting those on our ForCASP forum (http://predictioncenter.org/forcasp/).
As you have been informed last week, we had initiated a ForCASP discussion on the evaluation measures for the model accuracy assessment category. Today we are adding a new topic - Assembly prediction. Other categories will follow shortly. We hope for your active participation in these discussions.
Information for server group leaders: we will start dry runs to check server connectivity and correctness of format in two weeks from now. To avoid missing the first CASP13 targets, please make sure your servers are registered by then.
Also, we will be holding at least two webinars to better inform you about the nature of the provided experimental sparse data in the data-assisted categories. The first webinar on SAXS and sparse NMR data is planned for April 23, at 8am California time (PDT), followed by a second session and 5pm PDT. The data providers, Greg Hura and Susan Tsutakawa (SAXS), and Gaetano Montelione (NMR) will briefly talk about the theory behind the data, the data format, and answer your questions.
Thanks for your interest in CASP, and we hope for an exciting new season!
CASP organizers
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| Discussion of the EMA evaluation measures has started on the ForCASP forum | (2018-3-27) |
Dear prospective CASP13 predictors,
We will be opening registration for the upcoming CASP13 experiment next week. The link to the registration form will be available from the main CASP13 webpage: http://predictioncenter.org/casp13/index.cgi
In the meantime, we are starting a series of discussions on evaluation approaches using the ForCASP forum (http://predictioncenter.org/forcasp/). These discussions were suggested at the town-hall session of the CASP12 conference as means to better communicate predictors' concerns about evaluation measures /process to future assessors.
The first prediction category to discuss is EMA (estimates of model accuracy). In the first post on this topic we suggest discussing three focus issues (see text): (F1) What to predict in global assessment; (F2) what to predict in local assessment; and (F3) what are the optimal evaluation functions. For quick reference, we provide a document with a description of the previous evaluation procedures, where we discuss additional open issues from the point of view of the organizers, and provide a feedback from the future assessor. We encourage all interested parties to post their thoughts so that the future assessors may take them into account in their assessments. For clarity, please mention section of the discussion you want to comment on (e.g., F1 or O5.2).
CASP organizers
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| CASP_Commons | (2018-3-15) |
CASP_Commons is now open for business: http://predictioncenter.org/casp_commons
30 research groups are awaiting results of our modeling (listed below).
Prediction Center Team
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Alan Rein (NIH/NCI)
Hsin-Fang Yang-Yen (IMB, Taiwan)
Andy Golden (NIH/NIDDK)
Brian Koepnick (UW, Baker Lab)
Jennifer West (NIH/NIDDK)
Howard Young (NIH/NCI)
Michael Maurizi (NIH/NCI)
Richard Michelmore (UC Davis)
Craig Myrum (NIH/NIA/IRP)
Qinglan Wang (NIH)
Stacey Harmer (UC Davis)
Arcady Mushegian (NSF/MCB, Virginia)
Oded Yarden (Hebrew University of Jerusalem)
Jake Liang (NIH/NIDDK)
Gareth Prosser (NIH/NIAID)
Daniella Schwartz (NIH/NIAMS)
Shioko Kimura (NIH/NCI)
Thomas Schneider (NIH)
Hufnagel, Robert (NIH/NEI)
Dakota Jacobs (NIH/NCI)
Luciano Abriata (Lousanne Poly)
Zhiyong Zhang (Rutgers)
Sonja Best (NIH/NIAID)
Hernan Folco (NIH/NCI)
Kelly Ten-Hagen (NIH/NIDCR)
Nilgun Tumer (Rutgers)
Udo Rudloff (NIH/NCI)
Dakota Jacobs (NIH/NCI)
Craig Myrum (NIH/NIA/IRP)
Claudia Kemper (NIH/NHLBI)
Cynthia Masison (NIH/NCI)
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| Opportunity to obtain the structure of a protein of interest in your research | (2018-1-12) |
We are happy to announce an opportunity to obtain the three-dimensional structure of proteins you are working on. Dr. Gaetano Montelione and colleagues (http://www-nmr.cabm.rutgers.edu) will determine structures of a few nominated proteins using NMR. Concurrently, these structures will be suggested as prediction targets in the forthcoming CASP13 experiment.
We are seeking proteins for which knowledge of structure will significantly advance research programs, and invite your nominations.
There are some restrictions on proteins that will be considered, imposed by the need to test structure modeling methods, and the limited resources available for experimental structure determination:
- No significant sequence homology to any of the structures in the PDB;
- 60-180 amino acid residues, preferably monomeric domain;
- Predicted to be ordered (i.e. not an intrinsically disordered protein);
- Soluble, non-disulfide bonded, globular protein which is predicted to fold inside of the cell ;
- No integral membrane proteins will be pursued in this cycle;
- Shallow sequence alignment, avoiding high-accuracy evolutionary covariance contact prediction.
Please provide a brief justification /explanation of your selection. Solved structures will be made publicly available.
Please submit your nominations to casp@predictioncenter.org with -CASP NMR structure determination- as subject line.
Feel free to share this with your colleagues.
The CASP Organizing Committee and the Montelione Laboratory
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| The 4th International Conference on Protein and RNA Structure Prediction Montego Bay, Jamaica December 4-8, 2017 | (2017-10-2) |
The message below is forwarded on behalf of the organizers of the 4th International Conference on Protein and RNA Structure Prediction Montego Bay, Jamaica December 4-8, 2017.
The 4th International Conference on Protein and RNA Structure Prediction will organized in Montego Bay, Jamaica from December 4 to December 8, 2017. The three previous conferences were organized in Xcaret near Cancun, Mexico by Zing Conferences in December 2011 and 2013, and in December 2015 in Punta Cana, Dominican Republic (without Zing).
The conference registration page is: http://www.cevs.ucdavis.edu/confreg/index.cfm?confid=917
We have highly rated all-inclusive resort in four star resort Sunset Splash in Montego Bay, Jamaica http://www.sunscaperesorts.com/splash that is one of the best on the island.
The Plenary Speakers include: John Moult, Nick Grishin, Andrzej Joachimiak, Ilya Vakser.
Already confirmed Invited Speakers include: Ron Elber, Tobin Sosnick, Peter Clote, Olivier Lichtarge, Jianpemg Ma, Wladek Minor, Jarek Meller, Ruxandra Dima, George Stan, Steffen Lindert, Alberto Perez, Nikolay Dokholyan, Franklin Hays, Andras Fiser, Yang Shen, Krzysztof Fidelis, Andriy Kryshtafovych, Ram Samudrala, Jianlin Cheng, Greg Chirikjan, Marek Cieplak, Uli Hansmann, Cezary Czaplewski, Maksim Kouza among others.
There are still speaking opportunities, so if you are interested to attend the conference and give a talk please contact Andrzej Kloczkowski: Andrzej.Kloczkowski@nationwidechildrens.org
The cost of early bird registration for this 5-day (4 nights) conference is $995 until October 15, 2017. After October 15, 2017 the cost of registration will increase to $1150. The cost of registration includes the price of the hotel and all meals and drinks in this all-inclusive venue. You may bring your spouse/accompanying person for an extra charge $103 per day. Children ages 0-12 sharing the room with two adults stay for free. The registration for students is $700 (the special code for student registration will be provided upon request). You may purchase also additional nights in the resort for early arrival and/or late departure at the conference registration website: http://www.cevs.ucdavis.edu/confreg/index.cfm?confid=917
The purpose of the 4th International Conference on Protein and RNA Structure Prediction is to bring together eminent scholars with expertise in various fields of computational modeling and prediction of structure, as well as experimentalists interested in these subjects. Since computational prediction methods continuously improve and evolve towards prediction of structure of more and more complicated biological objects our conference will cover also related topics, such prediction of structure of protein complexes, protein docking; prediction of intrinsically disordered regions in proteins, RNA structure prediction and modeling of RNA-protein assemblages. New methodologies for protein structure and function prediction will be discussed, such as physics-based approaches to the structure prediction, structural flexibility models, and development of new improved coarse-grained potentials.
We will gladly accept students and postdocs from your Lab to attend the conference and will offer them possibility to give short (contributing) talks.
If you have no other plans for Dec 4-8, 2017 please join us in Montego Bay.
See you in Montego Bay!
Best regards,
Andrzej Kloczkowski, Robert L. Jernigan and Eshel Faraggi
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| Conference in memory of Anna Tramontano, University of Rome, July 14, 2017 | (2017-6-28) |
Dear CASP Community:
We are writing to share the announcement of the upcoming Conference dedicated to the memory of Anna Tramontano. The Conference will be hosted by the University of Rome on July 14, 2017, which would have been Anna's sixtieth birthday. This is an open event. For details, see
http://predictioncenter.org/images/InMemory_of_AnnaTramontano720.jpg
CASP organizers
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| Anna Tramontano | (2017-3-10) |
Dear members of the CASP community,
We write with the very very sad news that Anna Tramontano died last night.
As you probably know, Anna was a mainstay of CASP from almost the beginning, first a predictor, then an assessor and then as an organizer. Her contribution was massive. She had extraordinary scientific insight, and an amazing ability to turn that insight into effective action both in her own research and in CASP. She ran a series of CASP conferences in Italy, she organized and hosted CASP planning meetings, she acted as chief editor of many CASP special issues of Proteins, she provided her own grant funds for many of these activities. She was always able to make wise and practical judgements on how to deal with problems and how to push CASP forward.
These formal acknowledgements fail to begin to convey what an extraordinary, marvelous, person she was, and what a privilege it was to know her and to work with her. She had an immensely strong personality that shone from her at all times - a world beating generosity of spirit that lit up a room. She was always someone to turn to in times of stress, knowing one would receive frank, honest, and wise counsel and help. We do not know what we will do without her.
John, Krzysztof, Andriy, and Torsten.
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| Target structures and results tables (text version only) have been posted on the web | (2016-12-2) |
Targets:
We have released structures of 40 CASP12 targets that were used in the evaluation. These targets (targets_T0), their domains (domains_T0), and the corresponding refinement targets (targets_TR), data-assisted targets (targets_Tsc) and oligomeric targets (targets_T0oligo) are now available through our CASP12 Data Archive repository - predictioncenter.org/download_area/CASP12/targets. Additionally, 31 targets are available to the assessors and were used in evaluation, but we cannot show their coordinates at this moment due to the confidentiality requests from their authors.
Result tables:
We have released results tables for regular targets, refinement targets and data-assisted targets through the CASP12 repository (http://predictioncenter.org/download_area/CASP12/SUMMARY_TABLES/). These results and the results of multimeric prediction, contact prediction and model accuracy prediction will be available as sortable tables and graphs through the Prediction Center web interface next Monday.
Abstracts and evaluation tables for the meeting:
We recommend that you download the CASP12 Abstract book and the text version of the automatic evaluation files to the laptop you take with you to the meeting, as we do not include CDs with these materials in your registration package. The conference hotel does have wireless Internet, but we cannot guarantee its reliability.
CASP organizers
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| Meeting program is available online | (2016-11-29) |
The complete program of the CASP12 meting is now available online at http://predictioncenter.org/casp12/doc/CASP12_Meeting_Program.html.
By now, CASP organizers have contacted the most successful predictors to give talk(s) or participate in the round table(s). Follow-up emails from the assessors with the specific questions are to follow shortly. We realize that the invited authors most likely would like to see the coordinates of CASP12 structures to prepare their talks, but unfortunately we will not be able to release all of the coordinates due to the confidentiality requests from their authors. Even though, the authors did allow us to show the graphical presentations of the target structures that have not been released by the PDB yet and also to post the evaluation results (scores) to the web. We plan on releasing those this coming Friday, December 2.
CASP12 organizers
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| CASP 12 Gaeta Italy Last minute registrations /posters | (2016-11-23) |
This is a reminder that registration for CASP 12 in Gaeta, Italy, Dec. 10-13, 2016 remains open but we are finalizing the hotel lists. This will be an exciting meeting in a venue located mid-coast, between Rome and Naples (also see our note from October 6, http://www.predictioncenter.org/news.cgi#264). If you plan to register, please do so shortly. If you have any registration related questions, please contact the Prediction Center at: casp@predictioncenter.org.
Information about the meeting: http://www.predictioncenter.org/casp12/meeting.cgi
Registration website: http://cevs.ucdavis.edu/confreg/reg/index.cfm?confid=851
Note to poster presenters: The size of the posters 70x100 cm, oriented in Portrait mode.
CASP organizers
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| CASP job fair | (2016-11-16) |
Dear CASP participants,
as we did in the past, we would like to organize a job fair at CASP.
Here is the idea:
If you have a position you would like to fill in your group, please send the ad (or a mail specifying the topic / requirements, etc) to anna.tramontano@uniroma1.it by December 1st possibly with Subject: Job fair offer
If you are looking for a job, please send your CV to anna.tramontano@uniroma1.it by December 1st possibly with Subject: Job fair application.
We will next send the CVs of applicants to people advertising positions and, if the latter are interested in interviewing any of the potential candidates, we will organize a place and time and provide you with an agenda.
Looking forward to receiving your mails.
CASP organizers
--------------------------------------------------------------------------------------------
Anna Tramontano
Department of Physics
Sapienza University of Rome
P.le Aldo Moro, 5
00185 Rome
Tel: +39 06 49914550
e-mail: Anna.Tramontano@uniroma1.it
URL: http://www.biocomputing.it
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| Voting for Methods Talks | (2016-11-3) |
Dear members of the CASP community,
As in previous three CASPs, in CASP12 we plan to have "methods talks" that would not be based entirely on group performance, but rather present new interesting ideas in the field.
Now, when the CASP12 Abstract book is available online (predictioncenter.org/casp12/doc/CASP12_Abstracts.pdf), we ask you to familiarize yourself with the descriptions of CASP12 methods, and nominate those of them that you consider innovative, having potential to improve the field, or otherwise interesting. Please send us an email with your nominee(s) by the coming Monday, November 7 (Subject: Abstract nomination). We will summarize your suggestions and provide you a list for final voting shortly afterwards.
CASP Organizers
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| CASP12 Early Bird registration deadline extended to Oct. 17th. | (2016-10-10) |
Due to several requests reporting delays with payment processing at home institutions we are extending the CASP12 Early Bird registration deadline to Monday, October 17th at 11:59PM Pacific.
CASP organizers
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| Early bird registration deadline for the CASP12 meeting is October 10th | (2016-10-6) |
A reminder that the deadline for early bird registration for the CASP12 meeting in Gaeta is now very close - next Monday October 10th.
The second planning meeting, in which the assessors present their preliminary findings to the organizers, was held a couple of weeks ago, and there is some pretty exciting stuff. In particular, looks like substantial improvement in average "new fold" model accuracy, probably due to the new co-evolution methods. The new "is the model as good as experiment for understanding function" category has a team of four assessors, led by Russ Altman, and should produce substantial insights. Very intriguing comparisons between SAXS data, experimental structures, and models. Again we have a collaboration with CAPRI for modeling assemblies, with a more substantial body of data than previously. And, of course, many interesting results in comparative modeling, refinement, and accuracy estimation.
Registration: http://www.cevs.ucdavis.edu/confreg/index.cfm?confid=851&webid=4026
Specifics of the travel arrangements:
http://predictioncenter.org/casp12/meeting_directions.cgi
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| Reminder: Deadline for submititng CASP12 methods abstracts - TOMORROW | (2016-9-14) |
Dear CASP predictors,
To be included in the CASP12 Abstract Book, your abstract(s) should reach us not later than tomorrow, September 15.
CASP organizers
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| The CASP 12 meeting registration is now open. | (2016-9-9) |
The CASP 12 meeting registration is now open: http://www.cevs.ucdavis.edu/confreg/index.cfm?confid=851&webid=4026 .
Specifics of the travel arrangements can be found at:
http://predictioncenter.org/casp12/meeting_directions.cgi
Let us all meet in Gaeta in December!
CASP organizers
***
12th CASP Meeting
December 10-13th 2016, Gaeta (Italy)
Subject: State of the art of methods for predicting protein structure, assembly, and function from sequence.
Scientific context: Results of the 12th international CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiment.
Confirmed invited speakers:
Russ Altman - Stanford University - USA
Alexandre Bonvin - Utrecht University - NL
Guido Capitani - Paul Scherrer Institut - CH
Matteo Dal Peraro - Ecole Polytechnique Federale de Lausanne - CH
Edward H. Egelman - University of Virginia - USA
Francesco Gervasio - UCL - UK
Michael Levitt - Stanford University - USA
Organizers: John Moult (USA), Krzysztof Fidelis (USA), Andriy Kryshtafovych (USA), Torsten Schwede (CH) , Anna Tramontano (I),
Location:
The meeting will be held at Hotel Serapo (www. http://www.hotelserapo.com/en/), on the slopes of the Natural Park of Monte Orlando in a beautiful and panoramic corner overlooking Serapo Beach, very close to the city center and the old town of Gaeta.
The city itself, the so-called Ulysses Riviera, is embedded in a fascinating area, full of surprises, natural beauties, history, art and culture. It is conveniently located between Rome and Naples. It overlooks the Tyrrhenian Sea. Its history as a resort dates back to Imperial Rome. Nearby sites include the first-century BC mausoleum of general Lucius Munatius Plancus. Its old town is mostly medieval, showcased by narrow alleys, the massive 13th-century castle and the 12th-century Cathedral of Assunta e SantErasmo.
Registration:
Deadline for early bird registration: October 10th, 2016
Deadline for late registration: November 14th, 2016
Registration fees (***):
Separate room Shared room
Early bird registration US$ 975 / ~850 Euro US$ 870 / ~750 Euro
Late registration US$ 1,125 / ~1000 Euro US$ 1,020 / ~900 Euro
Accompanying person (*) US$ 340 / ~300 Euro
Extra day before or after the meeting (**): US$ 90 / ~80 Euro per person
(*) Includes accommodation and full board for the period of the conference and Gala Dinner.
(**) Includes accommodation and full board.
(***) Depending on the resources available, some students might be entitled to receive a partial refund of the registration fee. Eligible registered applicants will be contacted after the early registration deadline. The amount of reimbursement will depend upon available financial resources.
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| Please send in your CASP12 methods abstracts | (2016-8-22) |
Dear predictors,
We have opened the webpage for collecting methods abstracts. The deadline for submitting the abstracts is September 15, 2016. Please read the instructions carefully and address all the questions specified in the Abstract submission form (http://predictioncenter.org/casp12/abstracts.cgi). Please remember that, as usually, your contributions will be taken into account in choosing presentations for the meeting.
Please also be informed that we will be opening registration for the CASP12 meeting in Gaeta in the closest few days. A separate announcement will follow.
CASP organizers
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| New data-assisted target has been released | (2016-8-8) |
A new cross-linking assisted target, Tx892, has been released today. There will be no new cross-linking assisted targets in the closest two weeks.
CASP organizers
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| End of CASP12 regular prediction season | (2016-7-29) |
*** Regular targets
Today we closed for prediction the last regular CASP12 target - T0946. All in all, we released 82 targets including 56 all-group targets, and collected over 53,000 predictions. The Prediction Center and the assessors already got access to many of the CASP12 structures and are in the process of evaluating the submitted models.
*** Refinement targets
The last refinement target was released today. All in all, we have released a record high 42 targets in this category (cf 37 in CASP11) . The latest deadline for the refinement targets is August 17.
*** SAXS-assisted targets
Ten targets have been released in this category so far. Data on an additional target is expected early next week. That will be the last SAXS-assisted target in the scope of CASP12 experiment. We want to take an opportunity here and thank to Greg Hura and Susan Tsutakawa from Lawrence Berkeley Lab, who did SAXS data acquisition for the selected CASP12 targets.
*** Cross-linking assisted targets
This is an important new direction (pioneered in CASP11) and we have tried to obtain cross linking data on at least some of the CASP12 targets. As target sample acquisition /data collection is time consuming, only today we are able to release data on the first set of these targets, the T0894/895 complex. We currently have prospects for cross linking datasets on approximately 10 additional proteins. We will be releasing these progressively, as soon as we have the experimental data in hand. We will inform you by email of every new release and implement longer prediction windows (3-4 weeks) to allow for more flexibility in modeling during the summer months. We will provide assessment for as many of these targets as we can as part of the CASP12 experiment. We are also looking into the options of providing experimental data and assessment on cross linking assisted targets in the future, if interest in this area is sufficient.
CASP organizers
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| Penultimate week of target release | (2016-7-18) |
=== Refinement targets
This week we are releasing 5 more refinement targets: one on Monday and Tuesday, two on Wednesday and one more on Friday. Another five targets are expected for the last week.
=== Data-assisted targets
One SAXS-assisted target has been released today (Monday). We are hoping for another target later this week. So far we released 5 SAXS-assisted targets and no cross-linking targets. The logistics of the data-assisted experiment is quite complicated involving timely collaboration between several labs around the world in preparation of protein samples, their shipment, collection of data, data transfer and preparation of targets for release. We hope that by the end of July we will have around 10 data-assisted targets both in SAXS-assisted and cross-linking assisted categories, but it is also possible that we will not receive the data for all the targets that are currently in the works by then. In this case we will have to either extend the target release period or move the delayed targets to CASP ROLL. We will inform you about the decision closer to the end of the next week, when the situation clarifies.
=== Interface accuracy (IA) of multimeric predictions
Yesterday we received a couple of questions concerning predictions in this category. We think that they might be of interest to a wider community and provide them below.
Q1. Will the list of homo-oligomers be provided by the Prediction Center or should we submit for any targets we like?
A1. Predictions on homo-oligomer targets should be submitted for all targets that have a numeric value larger than 1 in the Oligo State column of the Target List page.
Q2. How many models can be submitted for each target (only one or up to five)?
A2. Only one.
CASP organizers
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| Two more regular targets; IA prediction only on your own quaternary models or from sequence | (2016-7-12) |
=== Two new regular targets (well, actually one)
Target T0947 was received just yesterday and we will have it in CASP12 as both - regular and SAXS-assisted target.
Target T0948 is a re-release of target T0916, which was originally suggested for prediction on June 14. The next day after the target release, on June 15, the structure of its homologue - 5B5R was released by the PDB. This essentially turned this target from a very challenging de novo target into a much easier homology modeling target. We can see the effect of the template release in the accuracy of submitted predictions - the models that were submitted early in the game (including all server models) are of poor quality, while some of the human models submitted after the template release are of substantially better quality. Since it is unfair to compare predictions generated under uneven starting conditions, we are canceling the original target T0916 and re-releasing it as a template-based modeling target T0948.
=== Interface accuracy (IA) category update
Based on your feedback to our poll, we will not be pursuing interface accuracy prediction for oligomeric models generated by other CASP12 groups. In this round of CASP we will limit this category to estimating accuracy of interfaces in your own multimeric predictions (IMODE 1), and predicting interfaces directly from sequence (IMODE 3). Please see the description of the adjusted IA format at http://predictioncenter.org/casp12/index.cgi?page=format#IA.
CASP organizers
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| End of regular target release | (2016-7-8) |
=== Regular target release summary
Today (July 8) we have released two last regular CASP12 targets - T0945 and T0946. All in all, in CASP12 we released 81 different regular targets, 55 of which were designated as human-expert targets. Six out of the eighty one targets were additionally re-released for multimeric prediction (as targets T0929-T0934), and one more target was re-released for all prediction due to the original sequence error (T0946 - see below).
=== Target T0946
Target T0946 is a re-release of target T0919 with the corrected sequence. The original target T0919 will be canceled for evaluation. The reason for the cancellation and re-release is discrepancy in the sequence of T0919 as originally deposited to the Prediction Center (May) and extracted from the coordinate file (today). The difference between the two sequences seems to be big enough to potentially influence the modeling outcome. Therefore we are re-running modeling for this protein with the corrected sequence (target T0946). Predictions in all categories will be accepted.
=== Refinement and data-assisted targets
As of today, 25 refinement targets and 4 data-assisted targets have been released. We will continue releasing refinement and data-assisted targets through the end of July. Next week we will release 5 refinement targets and hope to release one or two data-assisted targets (based on the availability of experimental data).
=== Re-released multimeric-only targets (T0929-T0934)
Since none of the re-released targets will appear in the PDB next week, we are extending deadlines for all of them by one more week to the full three weeks of prediction (or just slightly shorter than that). Please check the Target List page for the extended deadlines.
=== Interface accuracy (IA) of multimeric predictions
Based on your feedback, we want to clarify submission details for the new category. We expect your IA predictions to contain interface accuracy estimates of your OWN multimeric predictions in the format provided at http://predictioncenter.org/casp12/index.cgi?page=format#IA (similarly to the QAself subcategory in the evaluation of tertiary structure prediction).
In addition to this we can expand the IA prediction to include a more advanced mode of prediction where we will provide tarballs of oligomer models to evaluate, and you will predict reliability of residues belonging to interfaces in those models (conceptually similar to the QAlocal mode of prediction). Before doing that we would like to poll the community on how many groups are ready to take on such a challenge. Please write us a message by the next Tuesday if you will be able to generate interface probability estimates in this prediction mode by the end of July. We will announce whether we proceed with this mode of prediction in this round of CASP by the next Wednesday.
CASP organizers
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| Going into week 10 | (2016-6-30) |
=== Week 9 summary
Through the first 9 weeks of the prediction season we released 76 regular targets, 21 refinement targets and 4 data-assisted targets. Six targets were re-released for multimeric-only prediction. Almost 40,000 models have been collected.
=== Plans for week 10
There will be no targets on Monday, July 4. For the rest of the week we will have 6 targets - one on Tuesday and Wednesday and two on Thursday and Friday. These are planned to be the last regular targets of the CASP12 prediction season (unless the organizers get something really interesting during the next week). With such a schedule we should have all regular targets closed before the end of July.
=== Refinement targets
As usually, we plan to have one target a day for the week (Tuesday-Friday).
=== Data-assisted targets
One SAXS-assisted target is expected on Friday. Please note that we found it possible to extend the deadline for the first SAXS-assisted target Ts886 for another week - so please rush in your predictions for this target by the next Saturday (July 9).
=== Interface accuracy (IA) of multimeric predictions
As announced a couple of weeks ago, we are opening an interface prediction category for multimeric targets. The general IA format was described in the previous announcements. For the format details please consult: http://predictioncenter.org/casp12/index.cgi?page=format#IA.
You should have three weeks from today (until July 22) to send predictions in this category on all multimeric targets, including homomultimers and heteromultimers. Through these three weeks we will be closely tracking the PDB release schedule and if we learn about the public release of some of the related targets before the July 22 deadline, we will shorten the prediction window for those targets and communicate the message to you. As of now, only one multimeric target has been released by the PDB - T0860, and, obviously, no IA predictions will be accepted for this target.
Please note that the IA predictions for the heteromultimeric targets should be sent only on one of the subunits constituting a heteromultimer. This subunit is predefined by the organizers. The list of such 'leading subunits' for the 11 heteromultimeric CASP12 targets is provided below:
T0861 : complex T0861/T0862: A(1-323,T0861), B(1-239,T0862), C(1-323,T0861), D(1-239,T0862),
T0870 : complex T0861/T0862/T0870: A(1-32,T08613), B(1-239,T0862), C(1-323,T0861), D(1-239,T0862), E(1-138,T0870), F(1-138,T0870)
T0868 : complex T0868/T0869: A(1-161,T0868), B(1-120,T0869)
T0884 : complex T0884/T0885: A(1-75,T0884), B(1-116,T0885)
T0894 : complex T0894/T0895: A(1-324,T0894), B(1-129T0895,)
T0897 : complex T0897/T0898: A(1-285,T0897), B(1-169,T0898)
T0903 : complex T0903/T0904: B(1-382,T0903), H(1-382,T0903), R(1-341,T0904), L(1-341,T0904)
T0907 : complex T0907/T0908: A(1-315,T0907), B(1-137,T0908)
T0914 : complex T0914/T0915: A(1-337,T0914), B(1-161,T0915)
T0921 : complex T0921/T0922: A(1-149,T0921), B(1-96,T0922)
T0925 : complex T0925/T0926/T0927: A(1-87,T0925), B(1-88,T0926), C(1-91,T0927)
For example, for the complex T0925/T0926/T0927 (last line, second column in the colon-separated table above) the interface predictions should be sent only on target T0925 (first column of the same table) and designated as 'TARGET T0925'. The predictions for heteromultimeric targets should contain residues from constituting subunits properly labeled with chain IDs provided in the table above.
The predictions for homomultimeric targets can contain any upper case letters to designate different chains, and will be verified for residue range consistency only.
If you have any question on the new format or the submission procedure - please do not hesitate to send us an email. We hope that despite the short notice we will still be able to learn a few things from this interesting prediction experiment.
CASP organizers
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| Update to week 9 target release | (2016-6-24) |
We had announced last week that last Friday we have released a special multimeric-prediction only target T0929, which was essentially a re-release of the CASP12 target T0859. We start this week with five more targets like T0929. If you do not predict quaternary structure you may ignore them. These new targets are released because in the time that passed after the original target posting we received additional information on multimeric state of some of them or got coordinates from the target providers suggesting oligomeric state higher than a monomer. The Assembly assessor wants to check if knowing this additional oligomeric information helps predictors to build better multimeric models. Since these additional targets can be released by the PDB any time, we will assign a shorter prediction deadline to them and will track the PDB release schedule. The deadlines may be extended by one week if it deems safe with the PDB. To make it clear which targets had originally unknown oligo state and then were turned into targets with oligomeric state higher than 1, we marked those targets in the Target List table as ?/n, where n is the newly revealed oligo state. Also, we want to bring your attention to a minor change in the Target List table. As you know, symbol '1' in the column 'Oligo' of the original table used to mean 'either monomer or unknown'. Now we untangled these two scenarios leaving '1' only for the targets that are actually monomeric, while replacing 1 with a question mark for those with unknown oligo state.
Since we are releasing five targets today, there will be no targets on Tuesday. Starting Wednesday through Friday we will be releasing 6 targets to test generated models for molecular replacement (see our earlier announcement).
CASP organizers.
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| Week 8 and 9 plans | (2016-6-20) |
=== Week 7 summary
More than 30,000 models have been collected on 64 targets from 170 groups.
=== Plans for the remainder of the week 8 and week 9
Tomorrow (Thursday) we will have three targets (T0925-927) forming a hetero-trimer complex. You will notice that one of the subunits of the Thursday complex - T0926 is very similar in sequence to the Wednesday target T0924. We release these two as separate targets since the Wednesday target was solved as a homodimer, while the Thursday one was solved in complex with two other subunits. Finally, we will wrap up the week with a relatively easy target T0928 and a special multimeric-prediction only target T0929, which is essentially a re-release of the first CASP12 target - T0859. CASP organizers were recently informed that this target is a homodimer and want to check if knowing this information helps predictors to build a better multimeric model. Since this target can be released by the PDB any time, we will assign a shorter prediction deadline to it, which eventually can be extended if we get the green light from the PDB.
Next week (week 9) we plan to release 8-10 regular targets. Please note that these targets have a higher risk of being unsolved by the end of the evaluation season, as for all of them crystallographers collected data sets but could not solve the structures because they do not have a model for molecular replacement and were unable to get experimental phases. The idea is to use CASP models as starting points for the MR and see if these models could help crystallographers in solving these targets. If targets get solved they would be part of CASP12 experiment.
=== Refinement targets
This week we are releasing five refinement targets: one on Monday and Tuesday, two on Wednesday (forming a heterodimer) and one on Friday.
=== Data-assisted targets
One SAXS-assisted target will be released on Friday.
=== Quality assessment for multimeric predictions (interfaces)
Last week CASP organizers had a planning meeting with CAPRI organizers and the future CASP assessors and decided to introduce a separate prediction category, where predictors of the multimers (both mono- and hetero-) will be asked about the probability of specific residues belonging to the interchain interface(s). We are going to use the CAPRI definition to identify residues in the interface, which is 5A between the closest heavy atoms in the residues belonging to different chains.
Format of predictions in this IA (interface accuracy) category is the following:
FORMAT IA
residue_belonging_to_interface(ChainResnum) probability(0-1)
A56 0.84
A58 0.65
B10 0.76
B30 0.32
Probability values larger than 0.5 identify residues that are predicted to be more likely in the interface than not. In binary (two-class) evaluations, the value of 0.5 may be considered as the cutoff separating residues predicted to be in the interface from those that are not.
First targets in this category are expected next week.
CASP organizers.
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| Week 6 summary | (2016-6-10) |
=== Week 6 summary
More than 23,000 models have been collected on 55 targets from 166 groups.
=== Week 7 plans
Next week we will release 7 regular targets: a hetero-complex on Monday (two formal targets), two separate targets on Tuesday, and one target Wednesday through Friday.
=== Refinement targets
This week we released five refinement targets. Next week we will keep the same pace and release five more refinement targets (one target a day).
=== Data-assisted targets
Today we are releasing the first SAXS-assisted target - Ts886. Reminding that the data are posted at http://predictioncenter.org/download_area/CASP12/extra_experiments/ and the description of the provided files can be found at http://predictioncenter.org/casp12/doc/SAXS_Package_Reference_Page.html. Next week we are planning to release another SAXS-assisted target, this time for the complex T0894/895 (formally the target Ts894).
CASP organizers.
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| Week 5 summary | (2016-6-3) |
=== Week 5 summary
CASP12 is running full sail as we are finishing the fifth week of prediction. With 48 targets released and 165 groups contributing (including 80 servers) , we have collected more than 19,000 models already.
=== Week 6 plans
Next week we will release 7 regular targets: a hetero-complex on Monday (two formal targets), two separate targets on Tuesday, and one relatively large and challenging target Wednesday through Friday.
=== Refinement targets
Today (June 3) we have released the first target in the refinement category - TR862. More targets to follow next week. As usually, information about the released targets can be found at the CASP12 Target List page. Starting models can also be downloaded from the CASP12 archive at http://predictioncenter.org/download_area/CASP12/extra_experiments/.
=== Data-assisted targets
Next week we are also starting the data-assisted prediction experiment with the release of the first SAXS-assisted target. To familiarize yourself with the data and formats that will be provided in this type of prediction experiment - please follow the link http://predictioncenter.org/casp12/doc/SAXS_Package_Reference_Page.html. The SAXS data for the selected CASP12 targets will be generated at the SIBYLS beamline at Berkeley and posted for download at the CASP web server (http://predictioncenter.org/download_area/CASP12/extra_experiments/.)
CASP organizers.
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| Week 4 | (2016-5-23) |
Last week summary: 29 targets (including 17 all-group targets) released; 162 groups (including 80 servers) sending predictions; >10,000 predictions collected.
9 new regular targets will be released this week (May 23-27). We will have two targets per day, except for Friday, when we will have just one quite difficult and long (~500 res) target. Two Thursday targets are parts of the same heterocomplex: please check their target-specific web pages for details.
We want to remind you that in addition to the mainstream totally 'blind' prediction, we will be having several data-assisted experiments, including SAXS-assisted and cross-linking-assisted experiments on the selected CASP targets. Biologic samples of two CASP targets have been already shipped to the labs that are collaborating with us on this project, and a few more targets are in line. Hopefully in a couple of weeks we will have low resolution data from these experiments to suggest you for the data-assisted prediction. Details to follow.
CASP organizers
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| Going into week 3 | (2016-5-15) |
Week 2 summary: 212 groups registered; 19 targets released; 123 groups (including 80 servers) sending predictions; >5,000 predictions collected.
10 new regular targets will be released next week (two targets per day). Two Thursday targets are parts of the same heterocomplex - so, as usually, check target-specific web pages for instructions.
CASP organizers
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| T0860 | (2016-5-11) |
Dear assembly predictors,
We are approaching the first CASP12 'human expiration' deadline and want to remind you the rules for submitting assembly predictions for server-only targets. Target T0860, which expires tomorrow, was released as a server-only target and therefore will not be evaluated in the all-group track of tertiary structure prediction or contact prediction. At the same time, this target was announced at the CASP12 Target List webpage as a trimer and therefore it will be included in the evaluation of quaternary structure prediction for all groups, including human-expert groups.
For this particular target, we also wanted to inform you (even though some of you might have figured it out by themselves) that CASP12 target T0860 is very similar to the CASP11 human target T0795 and includes only a few extra residues. Even though you can see a picture of the T0795 MONOMER at the CASP11 website, neither pictures of a trimer or native coordinates (monomer or oligomer) were released so far. So you can take either model(s) generated in CASP11 on T0795, or server models generated in CASP12 on T0860, or your own CASP12 models and use those to build the trimer. Please also be informed that TR795 was also a target in the CASP11 refinement category, and therefore you can check how close were monomeric refinement models to the native structure in specific regions and try to improve those regions in the multimer.
CASP organizers
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| CASP12: week 2 targets | (2016-5-6) |
Dear CASPers,
The first week of CASP12 is behind us. Week 1 summary: 200 groups registered; 9 targets released; 66 groups (including 62 servers) sending predictions; ~1500 predictions collected. Tomorrow we will be sending the first queries to the registered QA servers.
10 new regular targets will be released next week (two per day). Three targets require special attention if you predict assemblies. The Monday targets T0868 and T0869 are subunits of a heterodimer complex. Please pay attention to the information provided in the Additional Information section of the target-specific web pages. If your method is limited to predicting only monomers, these two complex subunits should be treated as separate 'all-group' targets. The Tuesday target T0870 is a dimer and a part of a dimer of heterotrimers complex. Part of this complex (dimer of heterodimers) was released for prediction last week (targets T0861, T0862). T0870 is the third entity of this complex. Please pay attention to the Additional Information provided along with this target.
CASP organizers
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| First two targets are about to expire for server prediction | (2016-5-5) |
Dear TS and RR server participants,
This is just a friendly reminder that the first CASP12 targets - T0859 and T0860 are expiring in 3 hours (at noon PDT). Please check the server submission status page http://www.predictioncenter.org/casp12/status_n.cgi to make sure your predictions were accepted. If they were not - you have 3 hours to remedy the situation. No predictions will be accepted after the deadline.
CASP organizers
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| CASP12 starts next Monday, May 2 | (2016-4-28) |
Dear predictors,
1. As of today, more than 150 groups have registered for the CASP12 experiment and we are set to start the prediction season. If you are planning to participate, but have not registered yet - please do this as soon as possible. Today and tomorrow is also the last chance for server curators to resolve any remaining issues with connectivity of their servers to CASP distribution/ verification servers.
We will start CASP12 gently and release two short targets (one on a slightly harder side and another - on the easier) on May 2. Two more targets constituting a dimer of heterodimers complex will be released the next day. Please follow the submission instructions provided in the Additional Information section of target-specific webpages and remember that predictors of complexes and quaternary structure should submit their models for all submitted targets (please see a more detailed explanation and the example of the coming T0861/862 complex at our Q&A page: http://predictioncenter.org/casp12/index.cgi?page=QandA). There will be only one (but large and difficult) target on Wednesday, followed by two targets (one harder and one easier) on both, Thursday and Friday.
2. We want to inform you that we have finalized the place and dates for the CASP12 predictors' meeting. It will take place in Gaeta (Italy), in the already familiar to the seasoned CASP participants hotel Serapo. The meeting will run from December 10 through December 13, 2016. We are happy to announce that we can offer a significantly lower prices as originally expected (within 850 EURO including registration, accommodation and food for the whole conference).
Have an interesting prediction season!
CASP organizers
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| CASP12 dry run for servers - end of round 1 | (2016-4-25) |
We have finished the first round of checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. If you had registered a TS or RR server, but have not received at least one request from us for the target T0999 - please check your registration settings and contact us if in doubt. Also, if you do not see your prediction(s) as accepted in our server status page (http://predictioncenter.org/casp12/status_n.cgi), then either your prediction did not reach us or was rejected due to unregistered with CASP submission email or format issues.
Accuracy estimate servers (QA) will be tested starting tomorrow. If you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so immediately. During the tomorrow tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be suppressed.
A request to EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0999 - query received by MY_SERVER". Failing to do this may affect the timely addressing of unexpected connectivity failures.
CASP organizers
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| CASP12 dry run for servers | (2016-4-19) |
Dear CASP participants,
Registration for CASP12 is currently under way and, as of now, 78 research groups have already registered for the experiment. We are starting checking connectivity and correctness of prediction format for the servers in TS and RR categories tomorrow, April 20. Servers for estimation of model accuracy (QA) will be tested next week. Therefore, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so ASAP. We will be sending your servers a request to predict a test target, which, obviously, will not be a part of the CASP12 experiment. Please consult our format page (http://predictioncenter.org/casp12/index.cgi?page=format) for prediction format details.
CASP organizers
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| A message from the WeFold coordinator | (2016-4-13) |
We are very excited to announce the third WeFold experiment that will take place in the context of CASP12. WeFold is a project that brings people together to share ideas, methods, and decoys. WeFolds two main goals are: 1) to create hybrid pipelines from the combination of methods contributed by its participants and 2) to collaboratively identify and work on problems that hinder the advancement of the field.
We secured computing hours and storage from NERSC (National Energy Research Scientific Computing center), the WeFold gateway is fully functional (http://wefold.nersc.gov); everything is ready for your participation!
For all those who are coming back from WeFold/CASP11, please contact Silvia Crivelli (SNCrivelli@lbl.gov) and she will transfer your account to WeFold/CASP12; you do not need to register again. For all the newcomers, please register at http://wefold.nersc.gov and get an account. Once you get an account, you need to request to be a CASP participant. For more information, please contact Silvia Crivelli. Thank you!
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| CASP12 registration has started | (2016-4-5) |
Dear CASP Participants,
After a very interesting and promising CASP11 experiment, CASP organizers are anxious to see how the structure prediction field developed in the recent two years. Hope you as predictors also share our anxiety.
We have opened registration for a new round of CASP, which starts on May 1. Please go to our main web page (http://predictioncenter.org/casp12), familiarize yourself with the description of the upcoming CASP12 experiment and register for the prediction challenge.
If you have questions /comments /reservations about the registration or the scope of the experiment - please let us know by replying to this message.
Thanks for your interest - we hope for an exciting new CASP!
CASP organizers
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| Electron Microscopy DataBank challenges: a message from the organizing committee | (2016-3-2) |
This is a reminder posting about EMDataBank community-wide challenges to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing recommendations for validation criteria associated with every 3DEM map deposited to the EM Data Bank (EMDB) and map-derived model deposited to Protein Data Bank (PDB).
The two current challenges focus, respectively, on reconstruction and modelling at moderate to high resolution, with the goals of establishing benchmarks, comparing current practices, and evolving criteria for evaluation of results. Based on registrations we are anticipating a substantial number of map reconstructions and model coordinates.
Please note the following upcoming deadlines:
Map Challenge submissions: March 31, 2016.
Model Challenge submissions: April 31, 2016.
For more info visit http://challenges.emdatabank.org
EMDB challenges Organizing Committee
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| 6th CAPRI evaluation meeting to be held on April 17-19, 2016 in Tel-Aviv Israel | (2016-1-13) |
We are happy to announce that information about the meeting is now available on the meeting web-site: http://www.cs.tau.ac.il/conferences/CAPRI2016/
The program is still in flux, as speakers still need to be selected by the program committee amongst the best CAPRI performers for the evaluated targets, and other submitted abstracts.
The meeting is open to anyone interested in docking and modeling procedures.
We very much hope to see you all in Tel-Aviv in April 2016.
The CAPRI Management Committee.
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| 3rd International Conference on Protein and RNA Structure Prediction (formerly Zing) - Punta Cana, Dominican Republic, Dec 14-18, 2015 | (2015-10-27) |
The 3rd International Conference on Protein and RNA Structure Prediction will be organized in Punta Cana from December 14 to December 18, 2015. The two previous conferences were organized in Xcaret near Cancun, Mexico by Zing Conferences in December 2011 and 2013. We had a lot of problems with Zing when we organized two other conferences in 2014, and we stopped using their services. It took us a lot of time to learn how to do it on our own, and because of this the 3rd International Conference on Protein and RNA Structure Prediction has been organized at the last moment, with the help of CASP organizers.
The conference registration page is at: http://ces.ucdavis.edu/confreg/index.cfm?confid=789 .
We have excellent, highly rated all-inclusive resort in Punta Cana - Now Larimal Punta Cana: http://www.nowresorts.com/larimar?gclid=CNLwquTux8gCFYQ8aQodMw4Ceg - that is one of the best on the island.
The Plenary Speakers for our December conference include John Moult, Harold Scheraga and Nick Grishin. Other speakers might be announced later.
The Invited Speakers include: Sebastian Kmiecik, Ruxandra Dima, George Stan, Jarek Meller, Maksim Kouza, Jianlin Cheng, Ilya Vakser, Yang Chen, Adam Liwo, Marek Cieplak, Ralf Bundschuh, Adam Sieradzan, Michael Feig, Krzysztof Fidelis, Eshel Faraggi, Andriy Kryshtafovych, Uli Hansmann, Dima Kozakov, Faruck Morcos, Remo Rohs, Sylvia Crivelli, Samuel Handelman, among others.
We are still looking for more speakers, so if you are interested to attend a conference and give a talk - please contact Andrzej Kloczkowski: Andrzej.Kloczkowski@nationwidechildrens.org
The cost of the registration for this 5-day (4 nights) conference is $1075 until November 6, 2015. After Nov 6, 2015 the cost of registration will increase to $1275. The cost of registration includes the price of the hotel and all meals and drinks in this all-inclusive venue. This is significantly cheaper than the price of conferences organized currently by Zing. You can register on the UC Davis Conference and Event Services website: http://ces.ucdavis.edu/confreg/index.cfm?confid=789
The purpose of the 3rd International Conference on Protein and RNA Structure Prediction is to bring together eminent scholars with expertise in various fields of computational modeling and prediction of structure, as well as experimentalists interested in these subjects. Since computational prediction methods continuously improve and evolve towards prediction of structure of more and more complicated biological objects our conference will cover also related topics, such prediction of structure of protein complexes, protein docking; prediction of intrinsically disordered regions in proteins, RNA structure prediction and modeling of RNA-protein assemblages. New methodologies for protein structure and function prediction will be discussed, such as physics-based approaches to the structure prediction, structural flexibility models, and development of new improved coarse-grained potentials.
We will gladly accept students and postdocs from your Lab to attend the conference and will offer them possibility to give short (contributing) talks.
Sorry for a very short notice. Please help us to continue the tradition of having conferences on Protein and RNA structure prediction in-between CASP experiments. If you have no other plans for Dec 14-18, 2015 please join us in Punta Cana.
See you in Punta Cana!
Best regards,
Andrzej Kloczkowski and Eshel Faraggi
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| Ground transportation address | (2014-12-6) |
To conference attendees:
Please make sure you arrive at Paraiso Maya, not Lindo. The ground transportation address is: Iberostar Paraiso Maya, km 309 on the coast highway.
CASP organizers
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| Program, restaurants, posters | (2014-12-3) |
Program:
As you may have noticed, the final program of the meeting has been posted at our webpage.
Restaurants at the hotel:
Breakfast and lunch do not require a reservation. Also for dinner, there are restaurants at the hotel that do not require a reservation, but the majority of dinner restaurants do. Below we list the restaurants at Paraiso Lindo and Maya that are available to the Maya residents. You can make reservations with the concierge at each of the hotel pavilions in person when you arrive. Alternatively, we are told, one can make requests via email, stating their name and up to three nights of restaurant selections. Important: Please make your dinner reservations for 8:30 PM or later only, earlier times will be in conflict with the CASP11 sessions or events.
Paraiso LINDO; Paraiso MAYA;
Steakhouse EL FOGON Steakhouse EL RANCHO
Mediterranean EL FOGON Mediterranean LA MARINA
Mexican EL TAPATIO Mexican EL TAPATIO
Jamabalaya CAJUN Japanese LA GEISHA
Gourmet EL MUSEO Gourmet LETOILE
"In these last two mentioned restaurants (Gourmet), semiformal dress code for gentlemen long pants are required and only children 12 years and older are admitted."
The email address for Lindo restaurants is: chiefconcierge.lindo@iberostar.com.mx, and for Maya: chiefconcierge.maya@iberostar.com.mx
Posters:
In addition to the details mailed out yesterday - the poster board height is 95 cm (37 inches). No tacks can be used, just Velcro or double sided mounting tape. Please take some with you if you can, we might have some limited supply available if you cannot. The boards have a smooth plastic surface.
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| Final preparations for the meeting in Mexico | (2014-12-2) |
Transfers from /to Cancun airport:
There are taxis, shuttles, rental cars (sometimes very cheap + hotel parking is free). You may use the transportation services available at the airport, but this option is rather expensive. We have arranged for individual transfers with the company called CEO. The registration web page for transfers is www.ceo-mexico.com. Please use "CASP11" as the registration code. The cost is $30 per person one way. As is the recommendation of CEO, you may want to wait with booking the return transfer until you are at the hotel. A link to the pdf file explaining how CEO transfers work is posted at casp11 web page under the Meeting section.
Posters:
There will be two poster sessions during CASP11, the first one in the afternoon of December 8, and the second - December 9. If you have declared bringing a poster, a numbered location will be issued to you upon registration at the Convention Center. The nominal board space for a poster will be 30 x 34 inches or 75 x 86 cm (w x h). Taller posters may stick out above and below the board if they are sturdy enough (the height of the board is declared as 86 cm but judging from the available image it may actually be more than 86 cm). Authors of the odd numbered posters are expected to present on December 8, and of the even numbered, on December 9th. If you are bringing two posters, you should plan on presenting in the same assigned space consecutively on December 8th and 9th. Unregistered posters will be accepted only if (very limited) space is available or fellow presenters agree to adjust to accommodate additional posters: A stretch of 86 x 390 cm or 34 x 154 inches of poster board will be assigned four poster spaces but with smaller posters, it may accommodate five.
Results:
Yesterday we have released the results of CASP11 evaluations. Now you can check all calculated per-model scores and summary rankings of the participating groups. We want to emphasize that these data are only the results of automatic numerical evaluations at the Prediction Center; the official CASP11 results will be announced by the assessors at the meeting. For those who cannot attend - we plan on posting assessor presentations on the web shortly after the meeting.
Abstracts and evaluation tables:
We recommend that you download the CASP11 Abstract book and the text version of the automatic evaluation files to the laptop you take with you to the meeting, as we do not include CDs with these materials in your registration package. The conference resort does have wireless Internet, but we can not guarantee its reliability.
Program:
The detailed program of the meeting will be posted on the web tomorrow.
See you in Mexico soon,
CASP11 organizers
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| Target coordinates release | (2014-11-25) |
Dear CASP11 Predictors,
We have released coordinates of the majority of CASP11 targets - check our Data Archive (http://predictioncenter.org/download_area/CASP11/targets). As you will have noticed, coordinates of several targets (T0775, T0793, T0795, T0799, T0802, T0804, T0826, T0828, T0839) were not included in the tarballs due to the confidentiality requests from their authors. Even though, the authors allowed us to show graphical presentations of these structures, and we will include those in the complete set of CASP11 and CASP ROLL evaluation results, which will be released early next week.
See you in Mexico soon,
CASP11 organizers
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| Deadline to register for CASP11 is approaching! | (2014-10-24) |
Dear CASP Participants and Enthusiasts:
The final deadline to register for CASP11 is fast approaching! Rates are guaranteed only until November 1. After that they may increase to accommodate standard hotel prices, which are considerably higher. So if you have not already signed on, now is the time!
It promises to be an interesting meeting. In addition to all the usual fun of the fair, there will be sessions covering the new features of this CASP experiment, including modeling aided by experimental sparse data (X-linking and simulated NMR) and the CASP-CAPRI joint experiment on prediction of protein complexes. And early assessment results suggest exceptional results.
We are also delighted to announce that we have been able to upgrade the accommodation for the meeting without increasing the cost for you. We are moving to Iberostar Maya, a hotel that is part of the same Iberostar Paraiso all inclusive complex (located on the Riviera Maya, 25 min from Cancun airport).
We look forward to seeing you in this exciting new CASP location in December.
CASP organizers
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| Voting for the Methods Talks | (2014-10-23) |
Dear CASPers,
This message announces start of the voting on the Methods Talks. Please cast your votes for the methods you consider worth presenting at the meeting at http://predictioncenter.org/casp11/voting.cgi. For your convenience, we compiled a book of selected abstracts that contains communications just from the nominated groups (http://predictioncenter.org/casp11/doc/CASP11_Abstracts_nominated.pdf).
The voting facility will be open until Monday, Nov. 10. You should be able to track the voting summary after you cast your vote(s). Please refrain from voting for your own method or that of your close collaborators.
Authors of the methods that fared the most interesting for the community will be invited to talk at the CASP11 meeting.
CASP Organizers
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| Candidates for methods talks | (2014-10-13) |
Dear members of the CASP community,
As in previous two CASPs, in CASP11 we plan to have "methods talks" that would not be based entirely on group performance, but rather present new interesting ideas in the field.
Now, when the CASP11 Abstract book is available online (predictioncenter.org/casp11/doc/CASP11_Abstracts.pdf), we ask you to familiarize yourself with the descriptions of CASP11 methods, and nominate those of them that you consider innovative, having potential to improve the field, or otherwise interesting. Please send us an email with your nominee(s) by the next Monday, October 20. We will summarize your suggestions and provide you a list of the most interesting methods for voting.
CASP Organizers
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| Final week of submitting abstracts | (2014-9-12) |
Dear CASP predictors,
For inclusion your contribution in the CASP11 Abstract Book, please make sure your abstract(s) reach us not later than the next Friday, September 19.
CASP organizers
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| Early bird registration deadline extended for one more day | (2014-9-4) |
Due to organizational reasons, we are moving the early bird registration deadline forward by 24 hours. You have time by the end of Friday, September 5, to register for CASP11 meeting at the discounted rate.
CASP organizers
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| Reminder - only three days left to save on CASP11 registration | (2014-9-2) |
Dear CASP participants,
This is a friendly reminder that the Early Bird registration for the December in Mexico meeting ends in three days. If you want to take advantage of the discounted registration rates - please act quickly - the rates will go up $250 per person starting September 5.
CASP organizers
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| You can send us your methods abstracts now | (2014-8-20) |
Dear predictors,
Yesterday three events were marked on the CASP11 calendar.
1. We received the last CASP11 prediction. Thanks for all your hard work over the period of three and a half months! Now you can take a well deserved rest and we (organizers and assessors) will concentrate on assessing your almost 60000 predictions.
2. We opened the webpage for collecting methods abstracts. Please read the instructions carefully and address all the questions specified in the Abstract submission form (http://predictioncenter.org/casp11/abstracts.cgi). You have one month to compose and send us your abstracts. Please remember that, as usually, your contributions will be taken into account in choosing presentations for the meeting.
3. We stopped accepting applications from students /minorities for financial support to attend the CASP11 meeting. The organizing committee will consider your applications and notify fellowship recipients shortly after the closing of the "early bird" registration window - tentatively in the second decade of September.
Please be reminded that you have only two more weeks to take advantage of the discounted registration rates for the meeting. The rates will go up on September 5th.
CASP organizers
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| Last targets in contact-assisted category | (2014-8-11) |
Dear CASPers,
1. This week we are releasing the last 6 targets in contact-assisted categories Ts and Tc. Three of these targets (Tc826, Tc827 and Ts812) will be released today after closing the corresponding contact-assisted targets from the previous round, two more targets (Tc806 and Tc835) will be released tomorrow, and the last one - Tc832 - on Wednesday. Deadline for today's targets will be next Monday, August 18, and for the remaining three - August 19.
2. On the same day (August 19) we will stop accepting applications from students /minorities for financial support to attend the CASP meeting. Requirements for submitting the applications are available at the meeting registration page.
3. Shortly after receiving the last prediction (next week) we plan to start collecting methods abstracts. The Abstract Submission web page will be available through a link from the CASP11 main page.
CASP organizers
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| End of CASP11 regular prediction season | (2014-8-1) |
Dear CASP predictors,
Yesterday we closed the last three regular CASP11 targets. All in all, we released 100 targets including 55 all-group targets, and collected over 55,000 predictions. Thanks a lot to all of you, whose hard work and dedication made CASP11 yet another successful protein structure prediction experiment. The Prediction Center and the assessors already got access to many of the CASP11 structures and are in the process of evaluating the submitted models.
Even though the prediction season is over for the regular targets, the action is still in full swing for the special experiment targets. Today we have released the last targets in refinement (TR) and contact-assisted (Tp) categories. Also, no more targets will be released in the cross-linking assisted category (Tx). Summarizing, in CASP11 we have released 37 refinement targets (cf 28 in CASP10), 24 Tp targets (cf 15 in CASP10) and 4 Tx targets (new category).
Through August 11, we will continue posting tasks in Ts and Tc categories for those targets, where Tp and Tx challenges are currently active. The last CASP11 submission deadline in the assisted categories is planned for August 18.
CASP organizers
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| Updated file for Tx812 | (2014-7-24) |
Dear Tx predictors,
Please update the input file for target Tx812. The originally posted file was fine except it included a few contact pairs to non-existing residues 250-254 (should be 200-204 instead). If server groups want us to send a separate modeling request for this target - please let us know.
Thanks,
CASP organizers
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| CASP11 meeting registration is now open. | (2014-7-24) |
We are opening registration for the CASP11 meeting.
The discounted early bird cost is $1100 per person in a separate room and $950 in a shared room (double occupancy), if registration is completed by September 4. This includes registration fee, hotel accommodation and all meals for the time of the Conference. Participation fees will go up after September 4 to $1350 (separate room) and $1200 (shared).
We have negotiated discounted rates for extra nights and accompanying persons. Details are available at the UC Davis Conference Services registration page (link to which is provided at the bottom of the CASP11 meeting registration page - http://predictioncenter.org/casp11/meeting.cgi).
Please follow the registration guidelines closely. We reserve the right to cancel any registration not adhering to the guidelines, even when the system completes the registration and accepts payment.
We expect some funding for financial assistance to students and minorities, as well as to the most successful predictors. Awards will be made in the form of reimbursements for registration and/or accommodation costs starting in mid-September. Only registered participants will be considered for fellowships. To apply for a student/minority fellowship - please send us an email describing your role in developing CASP-participating method(s) and specify what you expect to gain from coming to the CASP meeting (one-two paragraphs). Please attach your short CV and specify the subject of the message as: CASP11 fellowships - yourname, groupname. The applications will be accepted until August 19, 2014.
CASP organizers
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| T0835, T0837 - reopening for human prediction | (2014-7-15) |
Targets T0835 and T0837, which were originally released as server-only targets, appeared to be more difficult for prediction than originally estimated and we are reopening them for human prediction and giving expert groups 10 more days for the modeling.
CASP organizers
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| CASP11 - week 12 update | (2014-7-11) |
=== Week 11 summary
We have finished the last full week of CASP11 target release with 95 targets and over 45,000 predictions.
=== Next week plans
We plan to release last five regular CASP11 targets next week Monday through Wednesday. One of these targets will be an all-group target, the rest - server only. After July 16 we will be releasing only refinement and contact-assisted targets.
=== Thank you to protein structure determination community
With the last targets already set for release, we are on our way to finish CASP11 season with 100 targets sharp! It was not an easy task for organizers to get such a rich testing set for you under the conditions of slowing PSI structure determination activity. Here we would like to take an opportunity and thank every single one crystallographer and NMR spectroscopist who participated and provided targets, be it one or thirty. The big share of targets was again obtained from the Structural Genomics centers, and we want to thank them for their continuous support of CASP. In particular, we want to recognize the JCSG, which provided over 30% of all CASP11 targets (see http://predictioncenter.org/casp11/numbers.cgi). We are also happy to report that 40% of the targets came from the non-SGI research groups, twice as many as in CASP10 and more than 3 times as many as in CASP9.
=== Meeting registration - update
Due to technical problems with the secure meeting registration page, we had to postpone opening of the meeting registration till the next week. A separate announcement will be sent once the meeting registration page becomes available.
CASP organizers
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| Tx781 - expires tomorrow | (2014-7-7) |
The first Tx target expires for prediction tomorrow. Below we provide some additional information regarding the cross-linking experiments that have been performed. Hope this information may be useful for predictors.
***
The cross-linker is hetero-bifunctional and reacts on one side with the side chains of K, S, T, Y via the amide and hydroxyl group, respectively. On the other side the cross-linker reacts indiscriminately with any C-H and N-H bond, be it in the side chain or backbone of any amino acid.
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| CASP11 - week 11 update | (2014-7-3) |
=== Week 10 summary
No targets will be released tomorrow, and we are finishing tenth CASP11 week with 85 targets and over 39,000 predictions.
=== Next week plans
We are almost done with releasing regular targets in CASP11. Next week will be the last full week of target release. We will suggest you another 10 targets, two per day, Monday through Friday. Four of these targets may be suitable for CAPRI. More targets are expected in the refinement and contact-assisted categories.
=== Meeting registration
We plan to start registration for CASP11 meeting next week. A separate announcement will be sent once the meeting registration page becomes available.
CASP organizers
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| Tx781 - extended prediction deadline | (2014-7-1) |
As promised, we are extending prediction window for Tx781 by one more week (until July 8).
CASP organizers
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| CASP11 - week 10 update | (2014-6-27) |
=== Week 9 summary
Ninth week concluded with 77 targets released and over 35,000 predictions accepted.
=== Cross-linking assisted targets; Tx781
This week we released the first x-linking-assisted target. Please be advised that the reported distance limit (25 Angstroms for Tx781) is between the CAs of corresponding residues.
Target Tx781 was released yesterday on a short prediction deadline as T0781"s structure was scheduled to appear in the PDB on July 2. Today we got the information that the coordinates will not be released on that date and thus we might be able to offer you one more week for prediction. To play it safe and be insured from any last minute surprises, we want to keep the July 1 deadline for now and encourage you to submit your predictions by that date, keeping in mind that most likely the deadline will be extended on July 2.
=== Next week plans
Eight regular targets will be released next week: two targets per day Monday through Thursday and no targets on Friday. Three of the next week targets may be suitable for CAPRI. Please pay attention to the posted information on the Wednesday targets T0840 and T0841 as they constitute a single heterodimer modeling entity. More targets are also expected to be released in the refinement and contact-assisted categories.
CASP organizers
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| T0796 re-release - STOPPED | (2014-6-27) |
Dear predictors,
Please disregard our earlier message on re-release of T0796 for human prediction. It will stay a server-only target and no additional experiments (refinement or contact-assisted) are planned for it.
CASP organizers
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| First Tx target - Tx781 has been released with only 5 days for prediction | (2014-6-26) |
Dear Predictors,
We are beginning a special experiment in contact assisted prediction to allow using actual experimental data (distance constraints from cross-linking experiments) to facilitate obtaining correct models (Tx targets). Considerable effort was put into making these tests possible (thanks to Juri Rappsilber"s experiments and cooperation from crystallographers providing protein samples). Normally, we will be giving you at least a full week for prediction of Tx targets. With this target, though, comes a shorter deadline as the structure will most likely be released by the PDB on July 2. We will inform the assessors about the shorter deadline for Tx781 and this may be taken into consideration in the assessment. Nevertheless, since we expect at most a few targets in this category, all the results will make part of CASP11 and be discussed at the meeting.
The released file is in the usual CASP contact data format. Due to the length of the linker, the limits are of up to 25 rather than the usual 8 Angstroms. The last column provides an estimated confidence level for the contact to be correct.
CASP organizers
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| CASP11 - week 9 update | (2014-6-20) |
=== Week 8 summary
Eighth week concluded with 69 targets, over 30,000 predictions and over 200 groups participating. Last Wednesday PDB has released a big batch of CASP targets. All these targets are marked with PDB codes in the Description column of our Target List. Those anxious to see how accurately they predicted these targets can compare now their models with the experimental structures.
=== Next week plans
Eight regular targets will be released next week. We will have two targets on Monday, Thursday and Friday and only one long and difficult target on Tuesday and Wednesday. No CAPRI targets planned for this week. More targets are expected to be released in the refinement and contact-assisted categories. We also hope to get data for the first target in Tx category (cross-linking assisted prediction).
CASP organizers
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| CASP11 - week 8 update | (2014-6-13) |
=== Week 7 summary
The FIFA World Cup has started, but we continue releasing targets :) . Seventh week concluded with 61 targets, over 24,000 predictions and just short of 200 groups participating.
=== T0803 re-release (June 13)
Target T0803 (originally server-only target) has been released for human prediction today with the June 24 deadline.
=== CASP11 disorder prediction termination
At the CASP10 predictors' meeting in Gaeta the community decided that we should proceed with the disorder prediction in CASP11 only if suitable targets will be available. The organizers tried hard to get the proper targets for disorder prediction, but all our efforts were unsuccessful. Under such circumstances we announce that we are terminating CASP11 prediction of disorder regions and apologize to the predictors, who invested their time in this category of prediction.
=== Next week plans
Eight regular targets will be released next week. We will have two targets Monday through Wednesday and only one target (but long and difficult) on Thursday and Friday. Please pay attention to the provided additional info, especially for the Wednesday target, T0825. The interest in modeling of this target will lie completely in predicting the dimer.
More targets are expected to be released in the refinement and contact-assisted categories.
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| CASP11 - week 7 update | (2014-6-6) |
=== Week 6 summary
We have finished sixth week with 51 targets released, 194 groups contributing, and over 19,000 predictions submitted.
=== Contact assisted prediction
The first two Ts targets (Ts761 and Ts763) are to expire on June 11, and we will release Tc challenges for the corresponding targets immediately afterwards. (reminding that Tc-type targets are those, where we will be providing information on the correctly predicted contacts in RR category). We want to warn you that we will have only 6 days for prediction of these two specific targets, as both of them will be released by the PDB on June 18.
=== Refinement targets
With two refinement targets released today, we are already at the mark of 11 TR targets. Note that today's targets, TR780 and TR280, come from two different domains of the same regular target, T0780. The two domains have a similar fold, but models for them have problems in different regions, and therefore we decided to release both as TR targets.
=== Next week plans
Next week we will release ten more regular targets, one harder and one easier per day. Four targets will be designated as CAPRI targets. We also expect more targets to be released in the refinement and contact-assisted categories.
CASP organizers
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| CASP11 meeting location | (2014-6-5) |
Dear CASP Participants,
We are happy to announce a new site for the CASP 11 meeting scheduled for December 7-10, 2014. The conference will be held at Paraiso Lindo hotel on the Riviera Maya, Mexico (http://www.iberostar.com/en/hotels/riviera-maya/iberostar-paraiso-lindo).
This may come as a surprise to those who saw our earlier announcement of the conference site in the Dominican Republic. The response from the CASP community was better than expected, and we decided to move the conference to a larger site. Although the resort on the Riviera Maya is normally more expensive, the Iberostar organization agreed to grant us the same favorable conditions that allow keeping the conference registration fees at the original level (for registration and all-inclusive accommodation in a double occupancy room - $950, single - $1100). The resort is conveniently accessed via Cancun International airport.
In compliance with the NIH requirement, the Paraiso Lindo hotel is family friendly. The special conference hotel rates will be available three days before and three days after the meeting. Registration for the conference is expected to open on July 1.
In addition to the climate and the sea, the Yucatan peninsula offers numerous attractions:
http://www.tripadvisor.com/Attractions-g659488-Activities-Riviera_Maya_Yucatan_Peninsula.html
http://www.visitmexico.com/en/mayan-riviera
We hope to see you all at CASP11 at the beautiful Paraiso Lindo.
CASP organizers
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| First Ts target - Ts761 | (2014-6-2) |
Dear predictors in contact-assisted categories,
With this message we want to bring your attention to the release of the first sparse experimental data assisted target - Ts761.
We expect that the new prediction experiment will show if data available in a typical NMR structure determination process can help improving the quality of structure models. For the Ts type of targets, we will be releasing information on simulated sparse NMR contacts that reflect the data available in the initial stages of the state-of-the-art NMR study of a large protein. The corresponding input files will be posted at predictioncenter.org/download_area/CASP11/extra_experiments/. Please note that some restraints in the released contact lists are ambiguous. For each NOESY peak, one or more distance restraints are provided, of which at least one is correct. Format of the Ts input file is similar to the CASP's RR format - please consult the README_Ts file (uploaded to the same directory as above) for a more detailed description.
CASP organizers
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| T0774 - reopening for human prediction | (2014-6-2) |
Target T0774, which was originally released as a server-only target, expired for prediction today (June 2). We have carried out preliminary evaluation of this target and it appeared to be more difficult than originally estimated. Therefore we are reopening T0774 for human prediction and giving expert groups 10 more days for modeling.
CASP organizers
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| CASP11 - week 6 update | (2014-5-30) |
=== Week 5 summary
We are finishing fifth week of CASP11 prediction with 40 targets released, 180 groups contributing, and 14,500 predictions submitted.
=== Cancellations
We had to cancel a very interesting target, T0791. It was solved by a competitor group and released with the PDB past Wednesday, May 28. Since the premature PDB release happened after the server deadline, we are canceling this target only for human and QA prediction. All server predictions and all DR predictions will be evaluated as usually.
=== Contact assisted prediction of tertiary structure
This week we released the first four targets (Tp761, 763, 767, 771, "p" stands for predicted) in the contact-assisted category. Next week we plan to release corresponding Ts targets ("s" stands for sparse) for two of those targets (761 and 763), and the following week - corresponding Tc targets ("c" stands for correct). Below we recapitulate the principles of contact-assisted prediction in CASP11.
In the current CASP, the contacts that we are releasing following the primary CASP 3D structure modeling experiment on a given target (i.e. the unassisted prediction) are different than those in CASP10. The general idea is to include more realistic scenarios where restraints are obtained from typically accessible sources (Tp, Ts and Tx below), rather than selected from structure. In addition we will also be providing sets of contacts selected with the knowledge of structure (Tc, below). The contact sets will be released only on targets without a clear homology to available structures, and will include:
Tp: Predicted three dimensional contacts, collected in the Contact Prediction (RR) category - release shortly after finishing the unassisted prediction;
Ts: Sparse NMR contacts (simulated, see below) - release immediately after finishing the Tp prediction (if not selected for Tx);
Tc: Predicted three dimensional contacts as in (A), but selected to include only correct contacts - release immediately after finishing the Ts prediction;
Tx: Contacts obtained from cross-linking mass spectroscopy studies (expected only in a few cases, where it is possible to collect experimental data) - release after the x-linking data is available; targets selected for the Tx dataset will not be used in Ts and Tc sets.
Simulated sparse NMR contacts: Provided contacts will be based on simulations carried out in Gaetano Montelione"s group (CASP10 assessor) and will reflect data available in the initial stage of an NMR study. For fairly large proteins (> 160 AA), typically data are collected on deuterated samples resulting in simplified spectra that are easier to assign. The corresponding constraints are sparse and usually not sufficient to refine the structure using standard NMR packages. The challenge for us is to either solve the structure using more sophisticated modeling techniques or to provide at least partially correct models, facilitating interpreting more complex NMR data sets.
X-linking studies: Contacts from x-linking mass spectrometry will be obtained from studies carried out in Juri Rappsilber"s group (Technical University of Berlin). We are actively pursuing these experimental datasets and currently have several targets lined up. Although we will do our best to obtain these datasets for CASP, we have to caution that at present none have been completed.
=== Refinement targets
Four more targets have been released this week in the refinement category.
Last week we warned you about the short deadline for one of the TR targets, TR759. The NESG Center (target source) and the PDB both agreed to extend the hold for T0759 for two more weeks, and now we can offer refinement groups the full 3 weeks for TR759 modeling (deadline has moved from June 2 to June 12).
=== Complexes
This week we released another hetero-multimer for prediction (T0797/798 tandem). Please check submission instructions in the "Additional information" section for these targets.
=== Next week plans
Next week we open the overall ninth hundred of CASP targets with release of 10 regular targets: T0800-T0809. As usually, we will have one harder and one easier target per day. Three targets will be designated as CAPRI targets. We also expect more targets to be released in the refinement and contact-assisted categories.
CASP organizers
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| CASP11 - week 5 update | (2014-5-23) |
=== Week 4 summary
CASP11 is running full sail as we are finishing the forth week of prediction. With 34 targets released and 175 groups contributing, we have crossed the 10,000 prediction mark today.
=== Refinement targets
This week we released one target in the refinement category, TR759. Some of you have noticed that we are on a tight schedule with this target expecting predictions not later that June 2. Unfortunately, that is all we can offer as the structure will be released from the PDB the very next day. Cases like that (shorter deadlines) may happen in the future (so always pay attention to the deadlines!), but one may expect them as exceptions rather than a rule.
=== Multimers
This week we released two hetero-multimers for prediction (T0787/788 tandem and T0791). Hetero-multimers are new for CASP, and we posted detailed instructions on how to submit the predictions in the "Additional information" section for specific targets. Nevertheless, we received two messages asking for further clarifications, and we thought that answers to them may be useful to a wider audience.
*Question 1. Our group is a human group and we predict only all-group targets. T0787 is an all-group target, but T0788 is server-only. What are we supposed to do here?
*Answer 1. If you predict only monomers for all targets, then you do what you usually do - submit your model for T0787 and ignore T0788. If your method is capable of predicting multimers, submit your prediction for both T0787 and T0788 before the "human" expiration deadline.
*Explanation 1. We designate targets as server-only if their monomeric prediction is expected to be easy and not worth spending the time of human groups. Target T0788 is one of such targets. It has a very high sequence identity to available structures (misses just a few residues) and the main interest lies in prediction its multimeric state in the T0787/788 complex. Therefore, human groups will be assessed on this target only in the context of predictability of the whole T0787/788 hexamer (we will ask CAPRI team to do this evaluation job for us). Another example is target T0792. This target seems to be quite easy for monomeric prediction but shows quite unusual dimerization. Therefore it was released as a server-only target, which nevertheless may be a very interesting target for human experts predicting quaternary structures.
In general, we encourage human groups to predict multimeric targets ("Oligo State" column >1 in the Target List) regardless of their status (all-group or server-only). Please refer to the Targets section in the description of CASP11 experiment (predictioncenter.org/casp11/) for details.
*Question 2. The T0787 and T0788 target descriptions say that we should concatenate the two trimers in a single file.
* Answer 2. No, you should submit models for these two targets in separate files as for usual CASP targets. What we meant was that we expect to get a full set of coordinates in the same frame of reference after we concatenate your respective models T0787TSxxx_1 and T0788TSxxx_1.
=== QA
We have canceled server-only target T0778 for QA prediction as its structure was solved by a non-CASP experimental group and released by the PDB this week. Server predictions in other categories are not affected by this premature release and will be assessed as normal.
=== Next week plans
Next week we will release 7 regular targets. On Monday, Tuesday and Friday we will post only one target, each of which will be relatively large (400+ residues) and not that easy for modeling. Wednesday will be as usual (one harder and one easier target) and on Thursday we plan to release another hetero-multimer (T0797/798) - please pay close attention to the additional information posted for these targets.
CASP organizers
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| CASP11 - week 4 update | (2014-5-16) |
We have finished three weeks of CASP11 with 24 targets released and over 6,000 predictions collected from 111 groups.
This week we released first two targets in the refinement category, TR760 and TR762. Please note that for the refinement targets we are not sending automatic queries to servers. If you want your server to receive automatic queries for refinement targets - please let us know and we will accommodate your request.
For the next week we have 10 more regular targets for you. Please check additional information that will be provided with the targets, especially for the two planned for the Wednesday release - T0787 and T0788. We also hope to release 1-2 extra experiment targets, most likely in the refinement category. Next week (Tuesday) we also close our first human target - T0759. Please be reminded that assessors may want to know which servers you used as starting points for your expert modeling and what useful things you can say about your specific models (see our previous messages). Ta make additional information in your predictions better searchable, please use
REMARK 1 for identifying starting server models
and
REMARK 2 for listing your model-specific comments.
These comments will be stripped from your predictions for the original evaluation (so that your identities are not revealed in any way to the assessors), and will be shown to the assessors only after they come up with their final conclusions on the results.
CASP organizers
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| CASP11 - week 3 update | (2014-5-9) |
We have finished two weeks of CASP11 with 14 targets released and over 2,500 predictions collected from 100 groups (out of almost 200 registered). For the next week we will have 10 more targets for you.
We want to remind you that we are publicly releasing the best 150 server models per target on the 8th day after the target release. The predictions are selected to this "best 150" list based on the results of the Prediction Center's a-priori model quality assessment method. The files with the best 150 models have the "stage2" suffix in their name, e.g. T0759.stage2.3D.srv.tar.gz. The tarballs are posted at http://predictioncenter.org/download_area/CASP11/server_predictions/ around noon PDT. CASP and CAPRI participants are welcome to use these models as starting points for their modeling with a credit to original servers. All server models are posted on the same web page 2 days after the "best 150" posting.
CASP organizers
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| Assessing biological relevance of models | (2014-5-5) |
Dear CASPers,
The first two days of CASP11 are behind us and we are starting a new prediction week.
As we informed you earlier, the assessors in CASP11 will try their best to assess the models from the perspective of how well these models address relevant biological questions. The things that assessors might be looking at are:
What a 3D model can tell about biological properties of a protein that a simple sequence alignment does not show?
What super family does this protein belong to?
What does a specific mutation do to structure and function?
Where/how does protein partner X interact?
Which residues should be mutated to disrupt interaction with binding partner X?
What is the binding specificity of this member of the protein family?
What loops might make good epitopes?
Where/how does molecule X bind?
Where are the domain boundaries?
How does alternative splicing affect structure and function?
We realize that these questions cannot be reliably answered without staging additional experiments (which is unlikely) and we do not expect these questions to be applied for all targets. But we do expect that at least for some of them the assessors will be able to provide their educated guesses and expert judgements on the listed subjects. For some targets, we may provide specific information that we have from the target providers (e.g., reason for solving the structure, why it is important, oligomerization state, any ligands bound, etc.) hoping that you might be able to use this additional info in your modeling approaches and, potentially, do something differently knowing these extra bits of information.
We are also encourage you to provide one-two lines of text in the REMARK field (especially for hard, likely New Fold targets) listing useful things that you can say about the specific model. Especially, assessors will be interested to hear what experiments can you suggest from unique properties of YOUR model (that "default" modeling methods don't have) that would possibly interest biologists.
CASP organizers
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| May 1 - start of CASP11 | (2014-4-29) |
Dear predictors,
As of today, over 150 groups are ready to start their CASP11 prediction marathon. If you are planning to participate, but have not registered yet - please do this as soon as possible. Tomorrow is also the last chance for server curators to resolve any remaining issues with connectivity of their servers to CASP distribution/ verification servers.
We will start CASP11 slow and release two relatively easy targets on the first day of prediction season, May 1. Two more targets (including a challenging one) will be released the next day, and 10 more - the next week, Monday through Friday. We are planning on keeping this pace of two targets per day for the whole CASP11 prediction season (subject to target availability).
For those of you, who plan to submit multimeric predictions and want to have them evaluated in CAPRI, please be reminded that CAPRI-eligible targets may be selected from both all-group and server-only targets. Therefore, if you registered a regular (non-server) group - please make sure that you submit your predictions on all CAPRI-eligible targets, including CASP11 server-only targets. Note that the human expiration date on server-only targets will be shorter than that on all-group targets and usually set to 10 days after the target release.
Wish you a great prediction season!
CASP organizers
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| WeFold announcement | (2014-4-29) |
The WeFold collaborative effort will run again this year for CASP11 and we would like to invite members of the CASP community to join in. This collaborative experiment lets different groups work on different components of the protein structure prediction pipeline (like contact predictions, sampling, refinement, and scoring) thus making it possible to leverage the diverse expertise of the participating groups. The collaboration is mediated by the science gateway http://wefold.nersc.gov that was developed by the National Energy Research Scientific Computing Center (NERSC) which also provides the computing resources. Thirteen labs participated in CASP10 using up more than 1.6 million computing hours and sharing 8.8 million models. We expect to have even more participants this year. You can see the list of participants so far here: http://wefold.nersc.gov/wordpress/about.
This year, WeFold is reaching out to the broader community of scientists. Besides our machine-learning experts who are also CASP participants, we are engaging members of the broader machine-learning community to help us develop new scoring functions. We plan to have a formidable selection of scoring functions that will be applied to the ranking of the hundreds of thousands of models shared by the WeFold community. To learn more about the project, please visit the WeFold gateway http://wefold.nersc.gov or contact Silvia Crivelli at SNCrivelli@lbl.gov.
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| CASP11 dry run for servers | (2014-4-15) |
Dear CASP participants,
Registration for CASP11 is currently under way and more than 60 research groups have already registered for the experiment. We are starting checking connectivity and correctness of prediction format for the servers in TS, RR and DR prediction categories on Thursday, April 17. Quality assessment (QA) servers will be tested next week. Therefore, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so ASAP. We will be sending your servers a request to predict a test target, which, obviously, will not be a part of the CASP11 experiment. Please consult our format page (http://predictioncenter.org/casp11/index.cgi?page=format) for prediction format details.
CASP organizers
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| CASP11 registration opens March 31 | (2014-3-30) |
Dear CASP Participants,
Exiting news: new CASP experiment is just around the corner! We hope that you are full of enthusiasm and anxiety (as we are) and have your computers greased and warmed up. The registration for CASP11 opens tomorrow, March 31, and the link to the registration pages will be available from the CASP11 main page:
http://predictioncenter.org/casp11.
Based on your feedback and keeping pace with the new developments in the field, we are refocusing the experiment by launching additional prediction challenges and introducing important changes to assessment. Detailed description of the experiment is available at the CASP11 main page; here we list the main changes that will be implemented in CASP11.
1. Assessment.
In refocusing towards greater emphasis on function, submitted models will be assessed on of how well they address relevant biological questions. We will do our best to present these questions to you up front. To this end we will collect the relevant information from target providers and their collaborators (reasons for solving the structure, functionally important regions, oligomerization state, any ligands likely to be bound, etc.). The assessors, especially the assessor in the template-based category, will analyze which models are the most helpful in clarifying these questions. In addition, the standard numerical evaluation of predictions will be carried out at the Prediction Center.
2. Collaboration with CAPRI (Critical Assessment of Protein Interactions).
We want to bring closer the two related communities with the aim of stimulating increased interest in modeling of protein interactions. Members of both the CASP and CAPRI communities will be invited to model the interfaces of protein complexes, homo-multimers and domain interactions in appropriate CASP11 targets (this will not require separate submissions, only the usual CASP predictions in the TS format). The results will be evaluated using the established CAPRI criteria. We plan to discuss the results of both experiments at the CASP11 conference.
The results will be evaluated using the established CAPRI criteria. We plan to discuss the results of both experiments at the CASP11 conference.
3. Details of prediction.
New assessment standards and challenges require additional information to be included in model submissions.
3.1. Specifics of the new function-oriented assessment (described in 1 above) requires inclusion of all ligands /co-factors in the submitted models. These ligands should be listed in the end of the model as HETATM records placed between the last TER and final END (details will be posted at the format page shortly).
3.2. In connection with item 2 (above), we strongly encourage submission of predictions as multimers, when applicable (information about the oligomeric state will be provided when available), so that the accuracy of inter-chain interfaces may be evaluated in CAPRI.
3.3. Following suggestions of CASP10 predictors meeting, we will request sensible prediction of atom errors (the B-factor column) in the TS predictions (predictions with fewer than 2 different B-factors will be rejected). A more judicious prediction of accuracy will help in assessing how useful is the model in answering biological questions.
4. New initiatives.
We will continue probing the extent to which sparse experimental data or contact predictions might improve the accuracy of models. For selected targets we will provide contact data obtained from prediction, experiment, or generated to simulate sparse experimental data. We plan to make available the following tests:
4.1. Modeling based on predicted contacts.
Following the regular target prediction, we will be releasing the top ~L/5 long-range contact predictions from the historically best CASP contact-prediction groups (L- target length). These predictions will be released for some of the more challenging targets and will include both correct and incorrect contacts. The aim of this exercise is to learn if contact predictions from the existing methods can help improve the quality of submitted models.
4.2 Modeling based on simulated sparse experimental data.
Following 4.1, we plan to release a bigger set of contact predictions simulated based on the target structure (provided we can obtain the coordinates in advance and have enough time for re-prediction). As in 4.1, the provided sets will contain both correct and incorrect contacts. The aim of this exercise is to learn if contact information from sparse experimental data can help improve the quality of structure models.
4.3. Structure prediction based on only the correct predicted contacts (filtered 4.1).
Will take place after completing 4.2. We will be releasing top ~L/5 correct long-range contacts from the historically best CASP contact-prediction groups. The aim of this exercise is to learn if contacts that can be identified by the best contact-prediction methods can help improving quality of structure models.
4.4. We are also exploring an option of obtaining real cross-linking data on selected CASP targets (using biological material from structure providers). If we succeed, we will provide these restraints in a separate test.
4.5. Evaluation of models based on a perfect alignment to the template.
For the TBM targets with significant alignment errors seen in the submitted models, we will be releasing the correct alignment to the best structural template found with the LGA program (please comment on what format of the input data would be the easiest to incorporate in your methods - LGA output, AL CASP format, FASTA format alignment). Obviously, this experiment also requires that the target structures are available at the time.
5. The meeting.
At the last two CASPs many of you suggested exploring new sites for the meeting. We listened and are taking the next CASP to a completely new location - the Caribbean. The price of attendance will be lower than that currently offered at Asilomar and the airfare for most participants will be comparable.
If you have questions /comments /reservations about the registration and the suggested changes - please let us know by replying to this message. Especially, we are interested in your relative level of interest in the contact assisted tests as outlined in Section 4 above.
Thanks for your interest - we hope for an exciting new CASP!
CASP organizers
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| Resuming CASP ROLL | (2013-1-22) |
Dear CASPers,
Best regards for all of you in the New Year!
Hoping that you had good rest after the CASP10 experiment and meeting, we are resuming CASP ROLL with two new targets later this week. We made changes to our target submission system so that every time a new CASP ROLL target is posted for prediction - a message is sent to the registered group leaders. This way you should be able to better track appearance of new targets in CASP ROLL.
Also, for those of you who did not make it to Gaeta, we posted all assessors' presentations and some of the keynote talks on the web. Enjoy!
CASP organizers
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| Predictors meeting in Gaeta | (2012-12-7) |
Dear CASP10 Participants,
On the last day of the Meeting we will have our regular Predictors get-together. In advance, I would like to ask you to send in any comments regarding the CASP process in general and the operations of the Prediction Center in particular, as well as to share any additional insights you may have.
We would also like to return to the issue of making our collective efforts more relevant to the biology community. In what way could we make our network more helpful in advising on and/or guiding the modeling process? Would you be willing to get involved?
Please direct your comments to kfidelis@ucdavis.edu
Hope to see you all very soon in Gaeta,
Krzysztof Fidelis
for CASP organizes
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| Release of CASP10 results | (2012-12-5) |
Dear CASP10 Predictors,
We have released results of the CASP10 and CASP ROLL experiments. You can check now interactive results tables and graphs, as well as the parsable data, including the text SUMMARY_TABLES. As you will have noticed, coordinates for two non-canceled targets (T0695 and T0739) are still under the lock according to the requests of their authors.
In the last minute preparations for the meeting, we recommend that you download the CASP10 Abstract book and the text version of the automatic evaluation files to the laptop you take with you to the meeting, as we do not include CDs with these materials in your registration package. Don't be scared with this warning - the hotel in Gaeta does have wireless Internet, but we can not guarantee it will hold the load of 150 bioinformaticians simultaneously browsing the online results.
There were also minor changes in the program of the meeting - please check the website for the latest version.
Thank you and see you in Gaeta,
CASP10 organizers
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| CASP10 program; last week of registration | (2012-11-26) |
Dear CASPers,
We are in the final stages of preparation for the CASP10 meeting in Gaeta. All the speakers have been invited and the program has crystallized. We have a lineup of outstanding speakers, in particular:
Keynote talks:
Janet Thornton - Predicting structure and function: from dreams to reality.
David Jones - The impact of evolutionary information on protein structure prediction: past, present and future.
Michael Levitt - Two decades of CASP: the future of modeling and prediction in structural biology.
Manfred Sippl - Who solved the folding problem?
Roland Dunbrack - Structural bioinformatics for protein structure prediction.
Joel Sussman - Disorder - past, present and future.
Nick Grishin - Predictive landscape of CASP.
David Baker - From protein structure modeling to protein design.
Assessors talks:
BK Lee - Free modeling, CASP Roll and contact-assisted assessment
Gaetano Montelione - Template-based assessment
David Jones - Refinement assessment
Best predictors talks:
Yang Zhang - TBM and FM
Jooyoung Lee - TBM
Chen Keasar - FM
Michael Feig - Refinement
Baker group - Contact-assisted prediction
Hongyj Zhou - Model quality assessment
Methods talks:
David Jones - PSICOV
George Khoury /Gaurav Chopra - WeFold
Chris Sander - EVFold
Firas Khatib - FoldIt
Jinbo Xu - Raptor
Andrzej Kloczkowski - Kloczkowski_lab
Besides these talks we will also have a job fair, roundtables, poster presentations and more. The detailed program of the meeting is available from the main CASP10 web page (http://predictioncenter.org/casp10/doc/CASP10_Meeting_Program.html). Please note that we still have a few places for the conference available, but this week is your last chance to register as we are closing the meeting registration on December 1 and will not have an onsite registration option in Gaeta.
See you in Gaeta soon,
CASP10 organizers
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| End of Methods Talks voting; talk invitations; Gaeta ride sharing | (2012-11-16) |
Dear CASP Participants,
1. Voting on methods is about to conclude. The voting facility http://predictioncenter.org/casp9/voting.cgi will be open only until the coming Monday, Nov. 19. So if you have not done so yet, please vote today or over the weekend. More than 400 opinions have been already recorded and we can already see several methods that are leading the popular vote. Please note that you will be able to see the voting summary after you cast your vote.
2. We will be sending out invitations to the best CASP10 predictors (assessor-nominated speakers) and your selected methods speakers next week. The program of the meeting will be available shortly after the finalizing the list of speakers.
3. Those coming to Gaeta have probably checked our web page *How tp reach Gaeta*
(http://predictioncenter.org/casp10/meeting_directions.cgi)
for advises on how to get to the meeting venue. Please note that if you are leaning towards choosing the shuttle option for direct transportation from a Rome airport directly to the hotel, you can try to arrange for a ride sharing. To help you with this, we have opened a topic *Ride sharing for Gaeta* at the ForCASP forum http://predictioncenter.org/forcasp/.
CASP organizers
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| Voting for the Methods Talks starts | (2012-11-9) |
Dear CASPers,
This message announces start of the voting on the Methods Talks. Please cast your votes for the methods you consider worth presenting at the meeting at http://predictioncenter.org/casp10/voting.cgi. For your convenience, we compiled a book of selected abstracts that contains communications just from the nominated groups (http://predictioncenter.org/casp10/doc/CASP10_Abstracts_selected.pdf).
The voting facility will be open until Monday, Nov. 19. You should be able to track the voting summary after you cast your vote(s). In the past we noticed a positive correlation between the method(s) supported and vote's geographical origin, so please refrain from voting for your own method or that of your close collaborators as we will be filtering out such votes.
Authors of the methods that fared the most interesting for the community will be invited to talk shortly after the voting closes.
CASP Organizers
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| End of Methods Talks nominations - tomorrow | (2012-11-8) |
Dear CASP participants,
This is a reminder that tomorrow we will post the final list of candidates for the Methods talks voting.
If you want to nominate someone - please do it asap. Methods abstracts are available at
predictioncenter.org/casp10/doc/CASP10_Abstracts.pdf.
We also recommend saving the Abstract book to your laptop as we will not be distributing CDs with
abstracts and results at the meeting. Text tables with the evaluation results will be available through
our website in the first week of December.
CASP Organizers
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| Nominating abstracts for voting; poster size | (2012-11-7) |
Dear CASPers,
Many CASP participants communicated to the organizers that the Methods Session at the CASP9 meeting was very useful and informative as the presenters concentrated on the details of their methods rather than their performance in the experiment. Following on that success, we are planning to have another Methods session at the coming CASP meeting where people with interesting methods will be able to share details of their work.
The assessors have compiled an extended list of groups that performed not necessarily best but at least relatively well at this CASP. and we will suggest these lists for the Methods talks voting the coming Friday. But before we do that, we ask you to browse the abstracts yourself and nominate those methods you consider innovative, having potential to improve the field, or otherwise interesting for inclusion in the voting lists. Please send us an email with your nominee(s). The organizers then will compare the lists and suggest you a coordinated list for voting.
Please note that in addition to this there will be a different session where people with the most interesting posters (as determined by a special jury) will be asked to give short presentations. Therefore we ask all poster presenters to be ready to give a short talk at the meeting. By the way - the maximum poster size is 70x100 cm. If you have not registered to bring a poster but still would like to do so, please let us know immediately.
CASP Organizers
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| CASP10 job fair | (2012-11-3) |
Dear CASPers,
As in CASP8 and CASP9, we would like to take advantage of the CASP10 meeting to help young scientists looking for a position in Computational Biology and potential group leaders to meet there.
We plan to have time set aside to get them together for interviews / informal meetings /etc.
If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 15th of November?
If you have positions available could you please send a mail with the advert (or a short description in any case) to anna.tramontano@uniroma1.it by the 15th of November?
PLEASE USE THE SUBJECT "CASP10 JOB FAIR" in your email.
As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.
Thank you very much.
The CASP organizers
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| CASP ROLL - new targets | (2012-10-8) |
Dear CASP ROLL participants,
After the post-CASP10 break we are resuming releasing targets for the rolling experiment. At the moment we have seven new targets, which will be gradually released starting tomorrow (2-3 targets per week). These targets will constitute a part of a new post-CASP10 cycle of the ROLL experiment.
CASP organizers
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| Sep.6 - early bird registration deadline; CASP fellowships letters | (2012-9-4) |
Dear CASP participants,
All recipients of CASP student fellowships have been identified and notified.
Please proceed with the registrations according to the instructions provided
in the award letters.
Also, please be reminded that the CASP early bird registration ends in two days.
CASP organizers
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| Abstract collection; meeting fellowships; early bird registration | (2012-8-21) |
1. Just three days ago we received the last CASP10 prediction, and today we start collecting methods abstracts. The Abstract Submission web page is available through a link from the CASP10 main page. Please read the instructions carefully and address all the questions in the form in your abstracts. The submission deadline is September 28th, 2012. Please remember that your contributions will be taken into account in choosing presentations for the meeting.
2. We would also like to remind you that this Friday, August 24th, we will stop accepting applications from students /minorities for financial support to attend the CASP meeting. Requirements for submitting the applications are available at the meeting registration page. All fellowship recipients will be notified by August 31.
3. If you want to take advantage of the discounted registration rates for the meeting - please act quickly as the "early bird" rates are in effect only until September 6th.
CASP organizers
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| End of CASP10 regular prediction; one last refinement target tomorrow | (2012-8-2) |
Yesterday we closed prediction for the last regular CASP10 target. The final CASP10 target statistics: 114 targets including 53 all-group targets. We expect the majority of CASP10 structures to be gradually released by the PDB in the next 5 weeks. We will be updating our target list weekly (on Wednesdays).
Tomorrow we will release the last target in CASP10 refinement experiment. With its release we will have 28 refinement targets, which is exactly twice as many as we had in CASP9.
There will be no more contact-guided targets in CASP10. All in all we were able to suggest you 15 targets in this new prediction category.
Thanks to all of you who made CASP10 yet another successful protein structure prediction experiment. Due to your dedication and the hard work we already received almost 65,000 predictions. Now it's time for the Prediction Center and the assessors' teams to evaluate them. We'll keep you posted...
CASP organizers
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| CASP10 meeting registration is now open | (2012-7-31) |
Dear CASP Participants,
The early bird registration for the CASP10 Meeting in Gaeta, Italy (Dec. 9-12, 2012) is now open via the UC Davis Conference and Event Services. The link to the registration form is available at http://www.predictioncenter.org/casp10.
CASP Organizers
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| Last CASP10 regular target has been released | (2012-7-17) |
Dear predictors,
Good news: we have released our last regular target today, reaching 114 targets, including 53 all-group targets, for the season. With the re-organization of the Structural Genomics centers, it was not an easy year to provide targets but in the end we reached the numbers we have planned. We would like to take this opportunity and acknowledge the crystallographers and NMR spectroscopists who participated. The main share of targets was again obtained from the Structural Genomics centers, and we want to thank them for their continuous support of CASP, especially the JCSG, which provided almost 40% of all CASP10 targets (see http://predictioncenter.org/casp10/numbers.cgi). We also want to emphasize that almost 20% of the targets this season came from the non-SGI research groups, almost twice as many as two years ago.
We will continue pushing tasks to the QA servers until the last server target expires and releasing refinement and contact-assisted targets until the end of the month. By the end of this week we plan to release at least 3 more refinement targets.
Based on the availability, we will also continue releasing challenging targets for testing free modeling methods to those groups that participate in the rolling CASP experiment. For your convenience, we will be sending alerts to CASP ROLL participants when new targets are released.
CASP Organizers
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| CASP10: week 11 update | (2012-7-10) |
Dear predictors,
1. CASP10 target release season is entering its final stage. We plan to release last regular all-group target tomorrow (July 11). We will continue releasing server-only targets through next Tuesday (July 17). If we receive a difficult target during the final release week, we will squeeze it into the schedule (with a slightly shorter than usual deadline) and notify you via the newsletter. After July 17 we will be releasing only refinement and contact-assisted targets.
2. We just learned that a copy-and-paste mistake encroached in the sequence of target T0725. You can notice two pseudo-repeat units there that in fact are not present in the native sequence. For the cleanness of the prediction experiment, we are canceling target T0725 and re-releasing the corrected sequence as a new target T0745. This target has been solved as a dimer.
CASP organizers
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| CASP10: week 9 update | (2012-6-28) |
Dear predictors,
We are finishing 9th week of CASP10 target release and are on track of having 100+ targets total, including 50+ 'all group' targets. As we approach the last two weeks of target release we ask you to make the last push in getting interesting targets for our experiment by contacting your experimental colleagues and asking them to submit potential targets to CASP right away.
We are also moving forward with refinement and contact-assisted targets, having ten of each already released. Please remember that we will continue releasing these targets through the whole month of July.
Next week there will be no targets on Wednesday, July 4.
CASP organizers
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| T0690 - long deadline target | (2012-6-9) |
Dear predictors,
We have reasons to believe that target T0690, which was originally released as a server-only target, is more difficult for prediction than originally thought. Therefore we move this target to the all-group category and extend its manual group prediction deadline by June 22.
CASP organizers
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| CASP10: week 6 update | (2012-6-8) |
Dear predictors,
We have crossed the equator in CASP10 target release. Seventy-one targets have been released, including 65 regular, 1 contact-assisted and 5 refinement targets. Next week we plan to release 3-4 new targets for contact-assisted prediction. We have evaluated results for the first CASP ROLL contact-assisted predictions and learned that releasing 4-5 contacts per target did not help much predictors in modeling. Therefore in CASP10 we will be releasing more contacts. We plan to release L/15 - L/10 contacts per target, where L is the target length. Please remember that we release not the contacts that are the most popular, but vice versa - the contacts (mainly long-range) that are important for folding but were missed by the vast majority of predictors. Contact information is provided in the "Additional Information" section of the target page and also posted as a separate file at http://predictioncenter.org/download_area/CASP10/extra_experiments/ .
Please also note that deadline for one of the CASP10 targets - T0678 - has been moved one day ahead, to June 10, as this target (4epz) is to be released by the PDB on June 11.
CASP organizers
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| CASP10: week 4 update | (2012-5-24) |
Dear predictors,
You might have noticed that the recently released target T0682 is too easy for inclusion in the all-group target set. This target, however, is quite unusual for modeling. Looking at it more closely, you will easily find a closely related template for homology modeling, but be aware that its structure has substantial structural errors. Relying only on that template would likely give you less than satisfactory results. We see this target as an exercise in homology modeling based on a structurally poor template + subsequent refinement. So, if you plan to participate in the refinement experiment, please send your predictions for this target as a regular submission. First normal CASP10 refinement targets are planned to be released within the next few days.
Next week we will be releasing targets as usually, starting on Monday.
CASP organizers
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| CASP10: week 3 update | (2012-5-16) |
Dear predictors,
You might have noticed that we have released a couple of challenging targets this week. We will have a few more by the end of this week.
We also wanted to let you know that these days the organizers, old CASP9 assessors and new CASP10 assessors are having a planning meeting. The future TBM assessor has brought up the issue of model completeness, specifically that the prediction field has matured to the point where we should be requesting that all backbone and side chain atoms are present and reasonably packed in the submitted template-based models. We will still accept incomplete models but we would like to let you know that in this round of CASP the C-alpha or backbone only models (TBM) may (and likely will) be penalized in the assessment. Also, the TBM assessor would like to encourage predictors to submit oligomeric models wherever possible.
CASP organizers
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| CASP10 - week 1; appeal for targets | (2012-5-2) |
Dear predictors,
CASP10 is already off and running and we are anticipating another exiting prediction season! We have released five targets in the first two days of the experiment, and plan to release four more by the end of the week. To start it gently, we will be releasing only relatively easy template-based modeling targets this week. The more difficult targets will be released starting next week.
Thanks to the Structural Genomics centers, we currently have a supply of targets large enough to run the first three weeks of prediction, at a 12 targets/week load. However, because of the shift of the big SG centers away from coverage of structure space, the majority of these structures appeared to be template-based and just 3 or 4 of them vaguely fall to the free modeling category. In CASP9, a substantial share of more difficult targets came from experimental groups outside the SGI centers, and we very much need your help this time again to contact the broader structural community with an appeal for targets. We need all sorts of targets but most of all:
* novel folds and membrane protein targets;
* template-based modeling targets with lower sequence identity to template, right down to undetectable;
* targets containing significant amounts of disordered structure.
One mechanism that worked well in previous CASPs: each prediction group beats the experimental bushes to find at least one target. Personal approaches work MUCH better than mass e-mailings. What we are asking is that you each approach at least one, more if possible, experimentalists, and make a direct, strong, personal plea that they provide a target, explaining why it is important. Please direct them to the target submission URL for details of the process: http://www.predictioncenter.org/casp10/targets_submission.cgi
OK, that's about it. Please get in touch if you have any questions or concerns.
Hoping for lots of targets,
CASP organizers
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| May 1 - first CASP10 targets; new CASP ROLL contact-guided targets | (2012-4-26) |
Dear CASPers,
We are in the last stages of preparation for the opening of the anniversary CASP season. The first CASP10 targets will be released next Tuesday, May 1. As of today, over 200 predictor groups have registered for CASP10; if you are planning to participate but have not registered yet - please do this as soon as you can. Even if you are a veteran CASP participant, we encourage you to reread the CASP10 format page, as the email address for submitting predictions has changed as well as the rules for submitting QA estimates. Also, now is about the last chance for server curators to resolve any remaining issues with connectivity of their servers to CASP distribution/ verification servers.
For those participating in CASP ROLL, we want to bring your attention to the fact that we released 3 structure-guided prediction targets during the last two days.
CASP organizers
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| Server dry run - third round on April 23 | (2012-4-20) |
Dear CASP10 participants,
We are happy to announce that the second round of testing servers is over and we were able to get practically all of the currently registered 87 servers properly connected and returning predictions in the correct format. There are still a few servers that either are not online yet or do not accept the parameters that our distribution server is sending to them. If you have not received a request from us or have not seen confirmation/rejection messages from our verification system - it should be something wrong with your connectivity or the parameters specified at the registration. Please get back to us as soon as you can to remedy the situation. We will be having our last round of servers dry testing next Monday.
CASP organizers
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| CASP10 dry run for servers | (2012-4-16) |
Dear Caspers,
As of today, 72 prediction servers have been registered for CASP10 experiment. We have started checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. We have sent them 1-3 requests to predict the test target T0921. If you had registered a TS, RR, DR or FN server, but have not received at least one request from us - please check your registration settings and contact us if in doubt. Quality assessment servers will be tested starting tomorrow afternoon (PST). We also plan to send one more modeling request to all registered non-QA servers tomorrow morning (PST). So, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so immediately. During the tomorrow tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be suppressed.
A request to all EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0921 - query received by MY_SERVER". Failing to do this will not prevent you from participation in CASP10 but will affect the timely addressing of unexpected connectivity failures. The prediction itself should be sent to the address specified in the field REPLY-E-MAIL of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).
CASP organizers
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| CASP ROLL - target update; CASP10 - registration continues | (2012-3-30) |
Today we have released our fifth special interest CASP ROLL target (Rc012). We are able to offer you 3 full weeks for the contact-assisted prediction of R0012. Information about the domain delineation and some contacts in this target is posted to the Rc012 target page.
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CASP10 registration continues with 120 groups already registered. If you plan to register a server for participation in CASP10, we ask you to do so at your earliest convenience as this will allow us some extra time to check the readiness of your server.
CASP organizers
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| CASP10 - registration | (2012-3-28) |
The registration for CASP10 experiment is now open. The link to the registration pages is available from the CASP10 main page: http://predictioncenter.org/casp10. The page also provides description of the experiment. Please read through as some of the rules have changed compared to CASP9, in particular, those pertaining to the release of server predictions and QA submission procedures. Detailed information on CASP10 prediction submission procedures and format is available from our format page: http://predictioncenter.org/casp10/index.cgi?page=format .
For convenience of the predictors who are currently participating in CASP ROLL, they have been enrolled also in CASP10 with the same group id, group name and PIN number. The current CASP ROLL participants should now be able to access their CASP10 registration data and make updates if necessary. Please note that by using this pre-registration procedure your group name can not be changed for CASP10; if this is imperative for you - you will have to register a new group with the desired name and inform us that you don't want your CASP ROLL group enrolled in CASP10. We have changed the CASP acceptance system so that the predictors participating in both experiments can submit their predictions for the targets selected for both experiments only once (to CASP10).
If you have any questions concerning the registration - please send them to our casp at predictioncenter account.
CASP organizers
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| Slightly shorter deadlines for R0012 and Rc007; CASP10 registration - March 28. | (2012-3-24) |
CASP ROLL.
We are reducing by a couple of days the prediction period for two of the CASP ROLL targets:
R0012: old deadline - March 30; new deadline - March 29
Rc007: old deadline - April 2; new deadline - March 30.
*****
CASP10.
We will be opening CASP10 registration on Wednesday, March 28.
*****
CASP10 - CASP ROLL compatibility issues.
As we have already announced, during the regular CASP10 prediction season (May-July) both experiments (CASP10 and CASP ROLL) would run in parallel. For convenience of the predictors who are currently participating in CASP ROLL, we will automatically enroll them in CASP10 with the same group id, group name and PIN number. This way we try to avoid confusion of your having two different group IDs and PIN numbers in the two experiments. If you are currently participating in CASP ROLL but do not plan to take part in CASP10 - please send us a message and we will skip your automatic CASP10 enrollment. After the automatic registration, the current CASP ROLL participants will be able to access their registration data and make updates if necessary (e.g., add information that a server already enrolled in CASP ROLL will also be sending QA or DR predictions in CASP10). Please note that you will not be allowed to change your group name for CASP10; if this is imperative for you - you will have to register a new group with the desired name in CASP10 and inform us that you don't want your CASP ROLL group enrolled in CASP10. In this case you would have to handle submissions separately for the groups registered for both experiments: we are currently changing the CASP system to allow sending predictions only once for the targets selected to both experiments.
CASP organizers
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| Halting automatic queries to servers for contact-assisted prediction | (2012-3-14) |
Dear CASP ROLL participants,
Yesterday we have polled the CASP ROLL server curators about the readiness of their servers for contact-assisted prediction. Based on their response, we conclude that the vast majority of servers do not have yet the functionality to automatically utilize provided contact information. Therefore, we will stop sending queries in this category to all servers. Please send us a message when your server is ready for contact-assisted prediction and we will resume sending automatic requests to your server(s).
Target update.
Today we have released our third target for contact-assisted prediction (Rc001). Please note that the deadline for re-prediction is 2-weeks.
Tomorrow we will release our 16th regular CASP ROLL target.
On Friday we will release the first target for the chemical shift (CS) guided prediction of an NMR structure (Rs003). Chemical shift information will be provided in a separate file (BMRB format) available for download from the predictioncenter.org/download_area/CASPROL/extra_experiments/ page. As with the contact-assisted prediction, we will NOT be sending queries to the CASP ROLL servers for the CS-guided targets unless you request us to do so.
CASP organizers
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| Contact-guided structure prediction in CASP ROLL | (2012-3-9) |
Dear CASPers,
The CASP ROLL experiment is in full swing with more than 50 groups contributing. With the release of today's target we are at the 15-target mark. CASP ROLL registration is still open and it is not too late to join the experiment.
We have recently polled the community concerning interest in the additional structure-guided prediction experiments (contact-guided structure prediction, chemical shifts-guided modeling of NMR structures and structure modeling based on molecular replacement using ab initio models and crystallographic diffraction data). The biggest interest was expressed for the contact-guided structure prediction. Therefore, we are going forward with this initiative next Monday. We will be releasing 3 to 5 long-range contacts for some of the more challenging targets, provided we can get coordinates in advance and have enough time (at least 2 weeks) for re-prediction. The definition of residues in contact will be the one used in CASP contact prediction category: 8A distance between C-beta atoms (or C-alpha for glycine). For release, we will select contacts based on the specifics of fold and the success in prediction of particular contacts. Priority will be given to contacts important for correct protein folding and those where fewer than 10% of predictors were able to identify them.
Targets will be called based on the name of the original target. For example, the target for contact-guided prediction of the regular CASP ROLL target R0010 will be called Rc010 (notice the small letter 'c' in target's name). Information about the new targets will be made available through the main experiment Target List page. Contact information will be provided at the target-specific pages under the Additional Information section and also as a separate file available for download from the predictioncenter.org/download_area/CASPROL/extra_experiments/ page. Format for releasing contacts will be as follows:
REMARK Rc010: CONTACT-GUIDED STRUCTURE PREDICTION
CONTACT_1: 167A:25C
CONTACT_2: 116L:77K
...
Predictions should be submitted according to the rules of the corresponding main experiment, i.e. for targets originating from the CASP_ROLL experiment, predictions should be sent using the CASP ROLL web submission form or by sending an email to the casprol account.
If you do not currently participate in CASP ROLL but would like to participate in contact-guided structure prediction, you should register for CASP ROLL first and then send us predictions using the assigned CASP ROLL group code.
We look forward to a successful contact-guided prediction experiment next week!
CASP organizers
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| Changes for CASP10 quality assessment category | (2012-2-22) |
Dear prospective CASP10 participants,
We have posted at the FORCASP site the suggested changes to the CASP10 QA prediction and evaluation procedures. Please follow this link to read the details:
http://predictioncenter.org/forcasp/viewtopic.php?f=24&t=463&sid=b451a5971d4596ba29a5d53d213bdc52
CASP organizers
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| Collaborative group initiative | (2012-2-14) |
Dear member of CASP community,
Silvia Crivelli (LBNL, UC Davis, and a member of this community since 1998) is organizing a collaborative group to participate in CASP10 and possibly in CASP ROLL if time permits. This collaborative experiment will let different groups or individuals work on different components of the protein structure prediction pipeline (like alignment, loop modeling, scoring, etc) thus making it possible to leverage expertise at a large scale. The initial goal is to focus on ab initio targets. Certain groups may want to participate in the collaborative effort for all the ab initio targets while others may want to do just a few of them.
If you would like to learn more about this effort please visit wefold.wordpress.com or contact Silvia directly at SNCrivelli@lbl.gov.
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| Extra CASP experiments | (2012-2-1) |
At the most recent CASP meeting, members of the modeling community suggested launching several additional experiments that would benefit developers of predictive methods. We have successfully started one of the suggested initiatives - Rolling CASP - for modeling of difficult FM targets. The first CASP ROLL targets are now reaching their deadlines, and we are considering further experiments with some of them. The purpose of this email is to determine which experiments there is sufficient interest in.
Please let us know which of the following you expect you would take part in:
1. Chemical shifts guided modeling of NMR structures.
2. Structure modeling based on molecular replacement with ab initio models and crystallographic diffraction data.
3. Structure modeling knowing a few (1-3: how many?) important long-range contacts, either randomly selected or based on possible results from lysine crosslinking experiments (please indicate whether one of both would be of interest).
CASP organizers
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| CASP ROLL targets | (2011-12-2) |
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The second CASP ROLL target will be released next Monday, December 5, 2011.
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| Rolling CASP experiment - Start | (2011-11-30) |
Dear Caspers,
This is the last call to register for the CASP ROLL experiment in time for the first target release. We are pleased to announce that 40+ groups, including 20 servers, have already registered for the experiment. We have run connectivity checks for all of the registered servers and the majority is ready to begin. If you still have problems with your registered server(s) or are planning on registering new ones today - we will be continuing debugging server issues starting at 8 am PST today, November 30. If you experience any problems with your server(s) please let us know ASAP.
All CASP ROLL targets will have 3-day deadline for server predictions and at least 3-week deadline for regular group predictions. If possible, we will set more distant deadlines for regular group predictions so that physics-based groups get more time for running their methods. Please be aware, though, that in the unlikely situation when a target is publicly exposed before the regular deadline (and after the 3-week soft deadline), only models received within the initial 3-week prediction window will be considered. Therefore we recommend submitting the best models you obtain within the 3-week prediction period first, and then resubmitting the final models before the regular deadline.
The first target will be released tomorrow, December 1, at 9 am PST and will have a 10-week regular (non-server) deadline. There is a good chance that we will have another target for release on December 2, and a couple more - the following week. We will send an appropriate message to the registered CASP ROLL participants.
Good luck!
CASP organizers
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| Rolling CASP experiment - Registration | (2011-11-23) |
We are opening registration for CASP ROLL experiment.
To register for the experiment, you will have to login to your Prediction Center (PC) account first (or register if you haven't done this before) and then go to the CASP ROLL web page and choose one of the five registration forms available there. Please, read the registration instructions to choose the appropriate form.
We ask that you register for the experiment at your earliest opportunity as we will be testing the connectivity with the registered CASP ROLL servers without any delay. We have already two targets at hand and are planning on releasing them for prediction on December 1, as it was announced earlier.
CASP organizers
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| Rolling CASP experiment | (2011-11-2) |
Dear CASP participants,
According to the suggestions of the CASP9 predictor meeting, we are announcing the Rolling CASP experiment.
Please follow the appropriate link from the Prediction Center main page http://predictioncenter.org/ for details.
We are also glad to inform you that there will be a regular CASP10 experiment in Spring-Summer of 2012 with the predictor meeting in December 2012 in Italy.
CASP organizers
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| A new local model quality visualization tool is now available | (2010-12-2) |
Dear CASP9 Predictors,
The current distribution of the CASP evaluation results which was just released comprises a new powerful local model quality visualization tool called the SphereGrinder, worth perhaps a few words of introduction.
The new approach is based on multiple local superpositions rather than a single global superposition or a series of global superpositions (as in GDT_TS). This avoids a possible shift error in some parts of the model. The general idea is to calculate RMSD inside a sphere centered on each amino acid in the target structure, i.e. to identify the atoms inside the sphere and calculate the superposition with the corresponding atoms of the model. In the visualization modes, a series of sphere radii are used for which the corresponding RMSDs are reported. Thus in one glance it is possible to assess the local accuracy of an entire model.
Another aim of developing this approach was to facilitate identification of any reasonable models submitted on FM targets. To this end models may be ranked by the number of residues for which the local structure does not deviate from target by more than a user defined RMSD cutoff. This particular option is available in the Cutoff mode.
The SphereGrinder (SG) is Java based and can be launched from the standard target pictogram: http://www.predictioncenter.org/casp9/results.cgi . A help file is available from inside the SG viewer. Please let us know if you have any suggestions on how to further improve this tool.
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| Fourth UCSC/QB3 Symposium on Bioinformatics - FREE!! | (2010-11-22) |
Fourth UCSC/QB3 Symposium on Bioinformatics
FREE!!
Engineering Auditorium
University of California, Santa Cruz
10-11 Dec 2010
As of 22 Nov 2010, we have only 3 abstracts and 21 registered attendees. I need at least 3 more abstracts to do a one-day conference (and 8-9 more for the originally planned 2-day conference). The speakers whose abstracts I have are Thomas Huber, Oscar Westesson, and Manel Camps. Three others have indicated a willingness to speak, but not sent me titles or abstracts. If they all follow through, I'll have enough for a one-day conference, but I'd really like 6 more speakers.
I also need at least 10 more attendees to register to make it worthwhile holding the meeting. The deadline for my decision on whether to hold the meeting or cancel it due to lack of interest is this weekend, so please send me your abstracts and register by Nov 24!
Kevin Karplus
Here is the original announcement:
All bioinformatics researchers and students are welcome to attend our free symposium. We would particularly like to invite all the attendees of CASP9 to stay on the Central Coast an extra couple of days for informal talks at UCSC.
The symposium is Friday Dec 10 and Saturday Dec 11. Researchers (primarily attendees of the CASP9 conference on prediction of protein structure, but also other bioinformatics researchers who are in the neighborhood) are invited to present any interesting work they have done recently as 40-minute talks (40 minutes plus 5 minutes for questions). Ideally, speakers will be talking about something different from any presentation they might give at CASP9. By scheduling the symposium after CASP there will be no "scooping" of CASP results.
There will be no refereeing of papers, no proceedings, and no money involved. We won't be arranging hotels, fancy meals, or any of the other things that can complicate running a conference. (It is the off-season for Santa Cruz hotels, so finding a reasonably-priced room should not be hard.) You can also search Google for Santa Cruz hotels.
QB3 (the California Institute for Quantitative Biosciences) has agreed to sponsor the coffee breaks and lunches at the symposium. In order for them to do this, we need fairly accurate counts of how many people will be attending. To this end we are asking that people who are coming register by Nov 24th using the form we have set up at pingg.
http://www.pingg.com/rsvp/f3xys5dp6573e88ng
Our reason for holding this conference is to get a bunch of interesting speakers to talk at UCSC. The incentive for others is an excuse to stay a little longer in California, and perhaps to talk about some more speculative work that isn't ready for archival conference or journal publication. Presenting material that has already been published but deserves wider dissemination is also very welcome.
Speakers are scheduled on a first-come-first-served basis (more or less). Prospective speakers should contact Kevin Karplus (karplus@soe.ucsc.edu ) and let him know
* your name and contact info
* your title and short abstract
* whether you can talk Friday, Saturday, or either.
This announcement can be found at
http://compbio.soe.ucsc.edu/workshop-2010.html
along with information about getting to UCSC and links to the
registration form.
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| Voting on the abstracts | (2010-11-18) |
Dear CASP Participants,
Voting on methods is about to conclude. The voting facility http://predictioncenter.org/casp9/voting.cgi will be open only until Monday, Nov. 22. So if you have not done so yet, please vote soon. Over 400 opinions have been recorded so far. Please note that you can see the voting summary after you cast your votes.
We also want to warn you that we are noticing a positive method /vote geographical origin correlation. So please try to refrain from supporting your own work more than once ;-)
CASP Organizers
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| Student /Postdoc input to CASP | (2010-11-15) |
Dear CASP Students /Postdocs
The CASP meeting is rapidly approaching. We will accept your input regarding the following until the end of this week.
1. About CASP in general: Are there any suggestions you would like to make regarding CASP sessions and particular topics you would like to see discussed.
2. About Student /Postdoc session in particular. Here Gaurav Chopra has prepared a special input web page. Please go to https://spreadsheets.google.com/viewform?formkey=dG0wbFY0aDA4SkI5TzZfLTRwRDljQ3c6MQ and send us your input.
Krzysztof Fidelis
for CASP Organizers
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| Voting on the abstracts | (2010-11-15) |
Dear CASP Participants,
We are planning to have a special Methods session at the coming CASP meeting where people with new/improved/interesting methods will share details of their work.
The assessors have compiled an extended list of groups that performed not necessarily best but at least relatively well at this CASP. We suggest that you check abstracts from these groups (http://predictioncenter.org/casp9/doc/Abstracts_selected.pdf) and select methods you consider innovative, having potential to improve the field, or otherwise interesting. Please cast your votes for these methods at http://predictioncenter.org/casp9/voting.cgi .
Please note that this will be a different session than the "Highlights" one, for which the speakers will be selected by the organizing committee based on recently published papers (see the recent announcement at our web site).
CASP Organizers
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| Posters at CASP | (2010-11-11) |
Dear CASP participants,
The maximum poster size will be 41 (Height) x 47 (Width) inches [1 inch = 2.54 cm]. If you have not registered to bring a poster but still would like to do so, please let us know immediately.
CASP Organizers
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| Student /Postdoc session at CASP | (2010-11-11) |
Hello CASP Students and Postdocs,
We are all excited about the CASP9 meeting in December. The CASP organizers want to present the students and postdocs with a unique opportunity where we can get the most out of the CASP meeting. We ask you to give inputs about making different sessions at CASP better in terms of what you think each session should discuss and how it should be presented. Please send us your suggestions!
Moreover, this year we are organizing a "Student Session" at CASP, which would be a perfect stage to ask questions to the leaders of the structure prediction community.
We ask for volunteers to help with the following to make the student session a success:
1. What would you like to see at this session - a Q&A session with panel of successful predictors, specific presentations etc. Please think about this in way so that you can benefit the most from this session.
2. Specifically, what questions would you want to get answered. It would be great to see a list of questions related to structure prediction and its applications or about the future of CASP and what is missing in the current successful methodologies.
3. Would you like a poster session at CASP, where the 10 best posters are picked to present a short talk (5 minutes each).
4. One predictor who you really want to see on the Q&A panel or give a specific presentation and WHY?
These are just a few ideas. It would be great to get more from all of you.
If you would like to volunteer to organize this session, please let us know by emailing us.
Best Regards,
Gaurav Chopra (gauravc@stanford.edu)
Krzysztof Fidelis (kfidelis@ucdavis.edu)
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| Influence future directions | (2010-11-11) |
Dear CASP Participants,
Since the first meeting in 1994, CASP has evolved considerably, including introducing new prediction categories, improving assessment techniques, and changing emphases of discussions during the meeting. To stay on track we ask you to look ahead, and help us correct things that do not quite work and recommend changes that would make CASP better. Therefore we request that you send us your suggestions in the next week.
We hope that your input will spawn a special session during the Asilomar meeting, including short individual presentations and discussion. Please write to Krzysztof Fidelis, kfidelis@ucdavis.edu, with specific suggestions.
We would also like to see this kind of issues discussed on the FORCASP forum in advance of the meeting.
Krzysztof Fidelis
for CASP Organizers
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| (2010-11-8) |
Dear CASPers,
We would like to introduce a new "highlight" session at CASP where published work relevant to our field will be presented.
To this end, we invite you to send us full papers that you have published, or that have been accepted for publication, in the last year and that are focused on biological/biomedical/biotechnological applications of protein structure prediction.
A committee will select the paper(s) to be presented at the meeting on the basis of their interest to the CASP audience, of the impact of the work on the field and on the likelihood that the work will make a good presentation.
We look forward to receive your submissions.
CASP Organizing committee
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| CASP9 job fair | (2010-10-28) |
Dear CASPers,
As in CASP8, we would like to take advantage of the CASP9 meeting to help young scientists looking for a position in Computational Biology meeting potential group leaders and vice versa. We plan to have time set aside to get them together for interviews / informal meetings /etc.
If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 12th of November?
If you have positions available could you please send a mail with the advert to anna.tramontano@uniroma1.it by the 12th of November?
As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.
Thank you very much,
The CASP organizers
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| Additional funds covering registration costs may be available for students and post-docs | (2010-10-14) |
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If you have already registered for the CASP meeting or are planning to register, and wish to be considered for the registration waiver - please send us your short CV, identifying yourself as a student or a post-doc.
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| Register for the CASP9 Meeting at Asilomar Now | (2010-9-24) |
Dear CASP Participant,
The Asilomar Meeting and Lodging Registration are now open at http://predictioncenter.org/casp9. Please note that the best Conference Registration rate (Early Bird) will only be available until October 3, 2010. Accommodation choices include the usual Asilomar room selections, i.e. Historic or Standard, and a selection of Single or Double occupancy (i.e. with a roommate). Accommodations are assigned on first come first served basis. Right now all selections are offered but please be aware that we may run out of the more popular choices or any on-site accommodation before the registration closes.
A limited number of registration/accommodation fellowships and a very limited number of travel fellowships will be available. However, registration and payment should not be made contingent on an accommodation or travel award. In case an award is granted, the registration fee, lodging fee, and/or travel costs will be reimbursed.
Please note that Financial Aid application deadline is October 3, 2010.
CASP Organizers
_______________________________________________________________
MEETING REGISTRATION
Meeting fees consist of a registration fee and a lodging fee for four nights (December 5-9, 2010) and have to be paid on line at the time of registration.
Registration Fee
Registration fee includes admission to all sessions, conference materials, coffee breaks, etc. The registration fees are as follows:
Early Bird Registration Special (AVAILABLE ONLY UNTIL October 3, 2010): $500
Regular Registration: $575
Late Registration (after October 22, 2010): $750
Lodging fee
Lodging fee includes hotel stay for four nights and all meals. The lodging fees are as follows:
Historic Room Double Occupancy: $424 (+ Registration fee)
Historic Room Single Occupancy: $628 (+ Registration fee)
Standard Room Double Occupancy: $488 (+ Registration fee)
Standard Room Single Occupancy: $796 (+ Registration fee)
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| Post-CASP workshop at UCSC - Dec. 10-11 | (2010-9-24) |
We're going to have the post-CASP workshop at UCSC on Friday Dec 10 and Saturday Dec 11 2010.
Information at http://compbio.soe.ucsc.edu/workshop-2010.html
It is once again free (sponsored by UCSC and QB3) but we are asking people to register, so that the organizers can provide coffee breaks and (most likely) lunches.
A PINGG invitation system for people to register is available through the web page.
Kevin Karplus
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| Methods abstracts | (2010-8-30) |
Dear CASP9 predictors,
It's abstracts time! The Abstract submission web page is available through the link from the CASP9 main page. Please read the instructions before submitting your abstract as format requirements have changed. The submission deadline is September 20, 2010. Please remember that your contributions will be taken into account in choosing some presentations at the meeting. Also, the predictors presenting posters at the meeting should be prepared to give a short presentation at one of the main sessions as some talks will be invited during the meeting based on the discussion of poster sessions.
Short update on the CASP9 evaluation progress. At this moment, the Prediction Center team and assessors are working at full load evaluating your predictions. As of today, the PDB have released structures for 78 CASP9 targets. You can check which targets have been already released by the PDB from our target list page. We also have more than a dozen structures at hand received directly from the experimentalists. The preliminary evaluations have been run on all of these structures. The assessors are at the final stages of defining domains and categorizing the targets so that the final evaluations can be compiled.
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| End of the CASP9 prediction season | (2010-7-30) |
Tomorrow is the deadline for submitting predictions for the remaining 3 out of 4 human/server CASP targets (T0643 expires next week). The final CASP9 target statistics: 129 targets including 60 human/server targets. We expect the majority of CASP9 structures to be gradually released by the PDB in the next 5 weeks. We will be updating our target list weekly (on Wednesdays). As of today, thirty-nine CASP9 targets have already been released by the PDB.
Also, today we have released the last (and we believe the most challenging one) target for the refinement. The details of the suggested target are as usually provided in the "Additional information" field of the target page. All in all, we have released 14 targets for the refinement experiment in CASP9. This is two targets more than we had in CASP8.
Now it's a good time to thank to all of you who made CASP9 yet another successful protein structure prediction experiment. We have already received a record number of 85,000 (!) predictions from you this season, and still counting. Thanks to your dedication and the hard work! Now it's time for our computers at the Prediction Center and the assessors' teams to evaluate the predictions. We'll keep you posted...
CASP9 organizers
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| T0622 - additional information | (2010-7-25) |
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T0622 expires for human prediction coming Tuesday. Those, who participate in the refinement experiment should have noticed the additional information we have posted about this target on the Refinement Target List page. We want to make sure that all the predictors are in equal conditions and noticed this info.
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| TR614 and TR622 | (2010-7-23) |
We released two more refinement targets today. Please note that even though we suggested two different models as starting points for TR614 refinement, it is technically only one refinement target and only one structure
should be provided in the prediction (no residue repetitions).
Next week we will conclude the release of the refinement targets. Hoping for 2-3 more targets depending on structure availability and suitability of the models for the refinement.
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| T0637 - reverted to server only target | (2010-7-21) |
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Target T0637 was independently solved by another crystallographic group and publicly released by the PDB today. We are reverting it back to the server only status.
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| July 17 - the last day of the target release (update - 2) | (2010-7-17) |
In the first two hours after releasing today's targets we have received a couple of requests to extend shorter than usual deadlines for the human/server targets released this week. We have discussed these requests and decided to slightly spill over into the first week of August in order to give you the full 3 weeks for prediction of T0637 and T0643.
CASP9 organizers
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| July 17 - the last day of the target release (update) | (2010-7-17) |
Just a few hours ago we received from our target depositors a sequence that shows no significant similarity to sequences of the PDB proteins. As hard prediction targets are getting more and more rare, it would be pity to waste such a good target. Therefore, in addition to the two server targets prepared for today's final release, we will be releasing another human/server target - T0643.
Sorry for the somewhat hectic last week of the target release season.
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| July 17 - the last day of the target release | (2010-7-16) |
Dear CASP9 participants,
As of today, July 16, we have released 126 targets for prediction including 61 in the human/server category. Please pay attention that the yesterday's target T0637 has been switched to the human/server category to compensate for the target reverted to the server only category yesterday. The last additions to the target list will be two more server targets that are scheduled for release tomorrow. And that would be it for regular prediction targets!
The CASP9 target statistics figures are well in accordance with the plan that we had for this round of CASP and very similar to the CASP8 figures (128/57). We wish to thank all the researches who were part of the CASP9 target collection effort, especially to the crystallographers and spectroscopists from the 3 Structural Genomics Centers (JCSG, NESG and MCSG), who provided more than 100 targets altogether for the CASP9 experiment.
We will continue pushing tasks to the QA servers until the last server target expires for prediction (July 21).
One more model was added to the refinement experiment today (TR606) and we expect to add a few more within the next two weeks.
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| T0555 is reverted to the server only targets | (2010-7-15) |
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Yesterday we announced about moving T0555 to the human/server category. On the same day, unluckily for us, the PDB released structure of 2ky4, which is our another target - T0553 and a close homologue of T0555. Under these circumstances prediction of T0555 by human-expert groups is not that challenging any more (for those who update their structural libraries regularly, of course). Therefore, we return T0555 back to the server only status and no new predictions will be accepted on this target.
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| Switching T0555 and T0562 to human/server prediction category | (2010-7-14) |
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Two more targets released in the "server only" prediction track, T0555 and T0562, appeared to be hard enough for modeling. We want to check if human-expert groups can do better on these targets and shifting them to the human/server prediction category. The human prediction deadlines for these targets are reset to July 31.
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| T0600 canceled for human predictions | (2010-7-12) |
We have canceled T0600 for human prediction as ribbon diagram of the structure had been prematurely exposed on the Internet. The target has been moved to the "server only" prediction category. Server predictions only will be assessed for this target.
Two more targets were released for the refinement today. We may potentially release one or two more later this week.
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| Week of July 12 - the last week of CASP9 target release | (2010-7-9) |
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We have almost finished releasing human/server targets for prediction in CASP9. We are at the number 57 so far. This week we released more targets of this type than usual in order to give you full 3 weeks to predict each of them. Next week is the last, 11th week of CASP9 target release and we will be releasing predominantly "server only" targets (based on their availability) with a shorter human deadline for them. If something really, really interesting shows up during this last week and it will be pity to waste such a target for server only prediction - we may release it as a human/server target. There will be at least one such a target released next Monday, but not more than 3 of them for the whole week.
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| Another starting model for TR517 and new refinement targets | (2010-6-28) |
While predictors can use any of the server models as the starting model for the refinement, we advise you which models turn to be the best so that the refinement can work better for you. Last week we released TR517 for refinement selecting one of the best server models as the starting model. This model had some missing residues while the best human model had all the residues in place. We want to provide you this model as a potentially better starting point for the refinement. Please recheck the Refinement Target List page for the new starting model TR517.
We have also released 3 new refinement targets and are planning on releasing another one tomorrow.
CASP organizers
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| CASP9 update - June 25 | (2010-6-25) |
Only three weeks are left for the release of targets this season. So, if someone knows a crystallographer or a NMR-spectroscopist who might have interesting targets for our experiment, please ask them to submit those to CASP right away.
This week we have released the first two targets for model refinement - TR517 and TR530
(http://predictioncenter.org/casp9/targetlist.cgi?view=refinement). The details of the suggested refinement targets are provided in the "Additional information" field for the targets. Coordinates of the starting models are available from the field "Template". Please, submit your refined models the same way you do for the regular predictions, remembering that names for the refinement targets start with "TR" instead of "T0".
Next week we are planning on adding several more targets to the refinement experiment and 10 targets for regular predictions.
CASP organizers
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| T0581 category change and Refinement targets | (2010-6-23) |
We originally released target T0581 as a server only target. After more careful consideration it appeared that this target is one of the more challenging targets to predict. We would like to suggest this target for prediction to human groups and shift it to human/server prediction category. To allow extra time for expert prediction, we are extending human deadline for T0581 by July 11.
We also will be releasing our first refinement targets this week. Please check our Refinement Target List link from the main CASP9 web page.
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| CASP9 update - May 14 | (2010-5-14) |
In our previous communication we stressed that human-expert structure predictors are recommended to concentrate their efforts on modeling of Human/Server targets. We want to emphasize here that all groups (including human-expert) that plan to predict in DR/RR/FN/QA categories are expected to submit their predictions on all targets, i.e. both - "Human/Server" and "Server only".
Disorder region predictors have been informed by the organizers that we had started enforcing the rule
that the residues predicted to be in the disordered state should have probability scores >0.5, while those in ordered state - less than 0.5. For those who are still planning to submit DR predictions - please make sure that your format comply with the requirements posted at our website.
Next Monday we will release one big target (887 residues) that will be followed by 10 to 12 other targets throughout the week.
CASP9 organizers
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| CASP update - May 7 | (2010-5-7) |
First week of CASP9 prediction season is over. We have released 14 targets. The vast majority of them were easy TBM targets. Next week you will find some harder targets in the human prediction category.
As of today, we have 125 groups (predominantly servers at this early stage) contributing models to the Prediction Center. You can always find the latest CASP statistics at http://predictioncenter.org/casp9/numbers.cgi .
In CASP9, we are planning on releasing between 50 and 60 targets for human-and-server prediction and approximately twice as much targets (depending on their availability) for server-only prediction. Assessors will be comparing all participating predictor groups on the subset of Human/Server targets and, additionally, the server groups on all released targets. The human-expert groups should concentrate on predicting structures for the Human/Server targets. Those, wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation emphasis will be placed on the "Human/Server" targets. Subject to availability, we will give priority to releasing targets containing low homology domains in the Human/Server track.
Reminding that we are accepting multimeric predictions this CASP. So far, we received such predictions from 9 servers.
Tarballs of tertiary structure models from servers are made publicly available at http://predictioncenter.org/download_area/CASP9/server_predictions/ the next day after a particular target is closed for server prediction, i.e. on the forth day after the target release, at 7:45am PDT. Approximately an hour later these tarballs are submitted to the quality assessment (QA) servers, which have an extra 3 days to submit their QA predictions. Deadline for human-expert QA predictions is the same as for all other types of prediction.
On the weekend days we will be submitting subsequent targets to the QA servers.
Next Monday we will release 2 new targets for prediction in all prediction categories.
Have a productive next week of CASP!
CASP organizers
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| May 3 - CASP9 starts | (2010-4-29) |
We are happy to inform you that as of today, April 29, we already have 100 human-expert groups and 125 automatic servers registered for the CASP9 experiment. With practically all CASP8 "winners" already on board and around 20 "new kids on the block", we are anticipating another exiting prediction season. Structural Genomics centers have started submitting sequences for potential targets to us and we have already prepared enough targets to run the first 2 weeks of the experiment at full load.
We will kick off the 9th round of CASP experiments with two relatively easy targets next Monday, May 2. These two targets will be followed by three targets Tuesday through Friday totaling 14 targets for the first week. To start it gently, we will not be releasing very hard for prediction targets this week. The first difficult targets are expected to be released starting the second week of the prediction season.
Reminding you that according to the decision of the CASP8 predictors' meeting we are reviving quaternary structure prediction in CASP9. We will advise you on the possible oligomeric state of the particular target protein if such information is furnished to us by the experimentalists. We want to stress out that this information should be taken just as an advice on the MOST PROBABLE quaternary state of the target as data on many of the CASP targets are coming to us when structure refinement is still in progress and therefore experimentalists can not be sure of the final assignments. Format for the multi-chain predictions is described at the CASP9 format page:
http://predictioncenter.org/casp9/index.cgi?page=format#TS , and shown in the Example 4 there.
Andriy Kryshtafovych
for CASP9 organizers
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| Second round of the dry run for servers | (2010-4-20) |
We have finished the first round of checking connectivity and format compatibility with the registered servers.
All non-QA servers were sent a query and we expected that all of them should have returned predictions by now (more than 3 days after the request). If your server did not get a query or did not send out a prediction - it's time to check for the problems and get in touch with the organizers. During the last 4 days we were able to identify and fix problems for the majority of 100+ servers registered for CASP9. Those server curators who haven't managed to make their servers work properly yet - don't hesitate to contact me in case you need help from the organizers' side.
Today we start a second round of the dry run for all registered CASP9 servers. In a few minutes we will be sending another test "target" to all non-QA servers. In the evening (Pacific Time) we will be sending a tarball from the first test "target" T0987 to the Quality Assesment servers.
Based on the first round of the dry run we can see that almost all of HTTP servers reply either with the web page or an email about their target receiving. This is not the case, though, for almost half of the email servers. So, email server curators: please, make sure that your servers reply to our distribution server casp8-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0987 - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. The prediction itself should be sent to the address specified in the REPLY-E-MAIL field of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).
Reminding you that during the dry run, you will be receiving both, acceptance and rejection messages from our verification server. During the regular CASP season it will be possible to check status of your server submissions through the link Server Predictions from the CASP9 web page: http://predictioncenter.org/casp9/status_n.cgi (link itself is already operational though not posted to the CASP9 web page yet).
Also, you can see all of your accepted predictions through the "My CASP9 profile" link from the CASP9 submenu on the left side of the CASP9 web page. The direct Model Viewer link will be available during the regular season from the CASP9 web page: http://predictioncenter.org/casp9/groups.cgi .
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| Server dry run has started | (2010-4-16) |
At this, first stage of the dry run we are testing servers returning predictions in all formats but QA. Quality assessment servers will be tested starting next Tuesday.
During these tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be turned off.
A request to all EMAIL-server curators: please, make sure that your servers reply to our distribution server casp8-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0987 - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. The prediction itself should be sent to the address specified in the field REPLY-E-MAIL of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).
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| Server dry run reminder | (2010-4-14) |
We were notified by several server curators that their servers are still in the process of preparation for CASP9 dry run. To allow them some extra time, we are postponing testing connectivity with the servers for two days. Also, we advise those caspers who plan to participate in server track but have not registered their servers yet to do it immediately. On Friday, April 16, 2010 we will send a test target (T0987) to the registered servers. Please respond as you would for CASP9 targets. Of course, these predictions will not be part of the CASP9 experiment.
We will be sending 3 variables to your server's submission URL (or email): the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results). For the quality assessment servers we will be sending the TARBALL-LOCATION variable instead of (or in addition to, if you specify so) the SEQUENCE. Please, make sure you provide the required parameters in your CASP8 server registration.
IMPORTANT THINGS TO REMEMBER
There will be no essential changes in the procedures for submitting targets and accepting predictions comparatively to the CASP8. For CASP novices, helpful information can be found below in this announcement and at http://predictioncenter.org/casp9/registration.cgi , http://predictioncenter.org/casp9/index.cgi?page=format .
1. Target distribution procedure for servers.
You will be receiving CASP9 queries from the distribution server in Davis casp8-meta@predictioncenter.org and the results will be collected directly by the Prediction Center. At the end of each week we will try to notify you about how many targets we plan to release the following week. Targets are planned to be released on business days only. We plan not to exceed a load of 3 targets per day for servers. Targets will be made available and requests to all servers will be sent around 9am PST. The submission engine will resend the query if it encounters obvious connecting problems (network timeouts, 'no response' etc.). Failures that go beyond that require special attention, but we'll make every effort to notify server curators ASAP if we suspect something is not working. The facility that allows checking data flow status by server predictors will also be available.
2. Server submission format.
Please submit your predictions in the standard CASP format. Your submissions will be immediately verified at time of submission. CASP warning and error messages will return directly and immediately to you, and will refer to the material you submitted, allowing you to respond in close to a server time frame, if necessary. Please note that, as in previous experiments, no prediction will be finally accepted by CASP until it passes CASP format verification. Please, consult the CASP format description page for details:
http://predictioncenter.org/casp9/index.cgi?page=format
3. The timeframe for server prediction acceptance is the following. All server groups have 72 hours since target distribution to return the prediction. Notifications will be sent to the server contact person's email address only in case of errors encountered. If your prediction doesn't pass the CASP verification system, you will need to correct your format and manually resubmit the corrected prediction to the email servers@predictioncenter.org within the original 72-hour window. After 72 hours no server predictions will be accepted or altered in any way. If you expect your server to work on prediction generation more than 72 hours, then we would advise you to register a regular (not server) prediction group for CASP9 instead.
In addition to notification emails, you will be able to check the submission status of your prediction through the Server Submission Status Page or through the Model Viewer facility.
CASP9 organizers
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| CASP9 - registration | (2010-3-29) |
The registration for CASP9 experiment is now open.
To register for the experiment, you will need to register with the Prediction Center (PC) first (if you haven't done this yet). At this step we will collect the basic registration information to be used for your participation in CASP9, all subsequent CASP experiments, between-CASP initiatives, and local services. The information provided by you will not be shared with anyone outside of the CASP system.
After you register with PC and login to our website, go to the CASP9 web page, where you will be able to register for the CASP9 experiment (a separate registration form under the CASP9 menu). You will find five separate registration forms there. Please, read the registration instructions and use the appropriate form.
We ask that you register with the Prediction Center at your earliest opportunity as we plan to release future CASP9-related news mainly through our website. We recommend that you select an option "Subscribe for Prediction Center newsletters" as in this case you will be receiving emails every time the news are posted on our website. This functionality was just recently added to our registration form. So, if you have registered earlier, please go to "My personal Data" link and select this option.
Also, we ask server group leaders to register as soon as possible as we are planning on testing the connectivity with the registered CASP9 servers starting April 14, 2010. The details of the dry run will be posted in the Message Board section of our website shortly (this section is available from both the Prediction Center home page and the CASP9 home page).
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| Blue Waters computer | (2009-12-14) |
Dear CASP Participant:
You might like to know that NSF is soliciting proposals for developing applications for the Blue Waters computer, due to come on line in the next year. As you know, there is a lot more interest in compute intensive methods of modeling protein structure than there was a few years, and this is an opportunity for those of you who can see possibilities in another couple of orders of magnitude of compute power to get unique resources. NIGMS is involved in this because they are interesting in encouraging projects in the area of protein folding and structure modeling, among others.
There is a webcast this Thursday, at which you can get more specifics. The NIH announcement (From Peter Preusch is as follows:
"NIGMS seeks your input on areas of science that would benefit from access to the latest generation high-performance computer. The Blue Waters petascale computing system, which is under construction by the National Center for Supercomputing Applications (NCSA) at the University of Illinois and funded by the National Science Foundation, will be the most powerful computer in the world when it comes on line in 2011. Details of the capabilities and architecture of the Blue Waters computing system are available at http://ncsa.uiuc.edu/BlueWaters.
This message is to alert you to the opportunity to apply for allocations of computing time on the Blue Waters computing system and to help organize collaborative groups to submit high-impact community applications for time on this new machine.
NIGMS is facilitating the formation of collaborative groups by:
1) Hosting a virtual workshop and applicant briefing videocast, NIGMS-NSF Briefing on Blue Waters High-Performance Computing Opportunities, Thursday, December 17, 2009 at 2:00 - 4:00 p.m. on the opportunity to apply to NSF for allocations of computing time on this important new resource.
2) Providing a Web site where you can share ideas on areas of science that could benefit from access to this resource and express your interest in joining or leading a group of scientists in an application to the NSF.
For additional information, visit http://www.nigms.nih.gov/bluewaters."
John Moult.
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| CASP9 meeting venue and dates | (2009-11-16) |
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CASP9 predictors' meeting will take place at the Asilomar Conference Center, Pacific Grove, California on December 5-9, 2010. Details of the future CASP9 experiment are available from the Prediction Center website.
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| CASP9 preliminary timetable | (2009-9-11) |
CASP9 experiment will be run May through July 2010.
Tentative dates are as follows:
March 30, 2010 - registration starts
April 14 - server "dry run" starts
May 3 - first targets will be released on or shortly after this date;
July 17 - last targets will be released not later than this date;
July 31 - prediction season ends;
December 2010 - the predictors meeting takes place at the Asilomar Conference Center in Pacific Grove, CA, USA.
CASP9 organizers
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| CASP8 domain definition and coordinates | (2008-11-21) |
We have released the official domain definitions and coordinates used for CASP8 evaluations. CASP8 Abstract book is also available from our website. Results of the automatic evaluation of the predictions will be available one week before the meeting.
CASP8 organizers
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| Arriving to Sardinia | (2008-11-16) |
A few important information about your travel to Sardinia:
Once you get to the airport of Cagliari, there are two ways to get to the hotel:
By bus: You take the ARST bus to Cagliari. the timetable can be found at http://www.sogaer.it/aeroporto/pullman/ . The cost is 2 Euro and the ticket can be bought at the automatic machines located in the hall of the airport.
The bus leaves you at the bus station in Cagliari. The station is on a square (Piazza Matteotti). You take the bus PF (direction Fiumini) and get out at the Hotel Setar stop (about 40 minutes). The ticket is 1 Euro.
You can take a taxi. The cost is about 40-50 Euro. Please only take official taxis and ask the driver the approximate cost to Hotel Setar.
There will probably be several people coming to CASP in your plane. You might want to share a taxi with them.
Meals included with your hotel room: from dinner on the day of arrival to lunch on day of departure. Any other arrangement should be made directly with the hotel. The cost of an extra lunch or dinner is 22 Euro.
The hotel bill should be settled upon arrival.
The hotel has wireless in all common areas and in most of the rooms.
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| CASP8 junior scientist session | (2008-10-28) |
Dear CASP Participants,
During the CASP8 meeting we will dedicate a special session to topics
suggested by junior scholars. We will also award a poster prize and invite
oral presentations. All students, postdoctoral associates, and others young
at heart are welcome to participate (only junior scholars will be eligible
for awards ;-)).
Our goal is to select areas that are of particular interest to the
community of young scientists. Please send suggestions /issues to be
discussed to Krzysztof Fidelis (kfidelis@ucdavis.edu). We would also
welcome volunteers wishing to help organize this session (contact Krzysztof).
Krzysztof Fidelis
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| CASP8 job fair | (2008-10-28) |
Dear CASPers,
we would like to take advantage of the CASP8 meeting to help young scientists looking for a position in Computational Biology meeting potential group leaders and vice versa.
We plan to organize an afternoon to get them together for interviews / informal meetings /etc.
If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 9th of November?
If you have positions available could you please send a mail with the advert to anna.tramontano@uniroma1.it by the 9th of November?
As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.
Thank you very much
The CASP organizers
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| CASP8 fellowships | (2008-10-15) |
We have now completed awarding CASP8 registration fee /lodging /travel fellowships and the recipients have been notified. The CASP8 speaker selection will be completed around Oct. 23. CASP8 speakers will be offered registration fee waivers, as well as lodging and travel reimbursements. At the same time we are extending early registration rate deadline to Oct. 27.
CASP8 organizers
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| CASP8 meeting registration; December 3 - 7, 2008; Sardinia, Italy | (2008-9-18) |
Registration for the CASP8 meeting is now open. We expect that this year we will be able to accommodate all the people wishing to participate. The Meeting Registration Form is available at:
http://predictioncenter.org/casp8/meeting_registration.cgi .
Meeting fees consist of a registration fee and a lodging fee for four nights (December 3-7). Rough estimate of total meeting fees (full board) for an academic participant is $880-$1050 depending on the accommodation choice. Details are provided in the registration form.
A limited number of accommodation fellowships and travel fellowships will be available. However, registration should not be made contingent on an accommodation or travel award.
Predictors attending the meeting are also required to ensure that a long abstract and a questionnaire (if requested by assessors) describing their group's method have also been submitted. A web page for submitting your abstract is available at http://predictioncenter.org/casp8/abstracts.cgi .
Please note that meeting registration will not be complete without submitting these materials.
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| Last 5 targets for refinement | (2008-8-2) |
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Five targets for the refinement experiment have been released yesterday and today. The details of the suggested refinement targets are provided in the pdb files for the starting models and in the "Additional information" field for the targets. All in all, we released 12 targets (14 domains) for the refinement experiment in CASP8 .
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| End of CASP8 target release | (2008-7-18) |
With the two server-only targets today, all CASP8 targets have been made available for prediction. In this round of CASP we have released 128 targets including 57 human/server targets. One target has been canceled so far. We expect the corresponding structures to be gradually released by the PDB. We regularly update our target list to indicate which targets have already appeared in the PDB. Please, check our target list for updates on Wednesdays. At this time we have structures for 34 CASP8 targets available.
Please note, that we will still be releasing targets for the refinement experiment. You may expect new refinement targets within the next two weeks. This week we have released 3 more targets for refinement.
CASP organizers
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| Human/server targets are over | (2008-7-12) |
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We have finished releasing human/server targets for prediction in CASP8. Last week we released more targets of this type than usual in order to give you full 3 weeks to predict each of them. All in all, we released 57 human/server targets in 11 weeks of the experiment or roughly 1 target per business day. Next week is the last week of CASP8 target release and we will be releasing "server only" targets.
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| T0472 - canceled for human predictions | (2008-7-9) |
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Target T0472 has been canceled for human predictions as the corresponding structure had been released by the PDB. The target is turned over to the "server only" status and will not be assessed in the human-track part of CASP8.
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| Refinement targets - 3 proteins (4 domains) | (2008-7-8) |
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Please, pay attention that 3 targets for the refinement experiment have been released today. The details of the suggested refinement targets are provided in the pdb files for the starting models and in the "Additional information" field for the targets.
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| T0465 - switching to human/server target | (2008-6-30) |
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We are switching T0465 over to human/server target. In order to provide enough time for human-regime modeling, we are adding 10 extra days to the prediction window for this target so that it will expire for human prediction on July 21.
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| No targets on July 4 | (2008-6-27) |
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Next week we will have no targets released on Friday. Next target release date after the holiday - July 7.
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| Extended timeframe groups | (2008-6-24) |
We are launching an additional service designed to help test methods requiring more time than the usual 3 weeks allowable in CASP8. Registering an additional “extended timeframe” group will provide a time stamp certifying the PRE-diction nature of the submitted models as well as CASP numerical evaluation results in the familiar format. Please note that the predictions sent by an "extended timeframe" group WILL NOT be part of the CASP8 experiment, WILL NOT be included in the final results tables and WILL NOT be assessed by the CASP assessors.
Please, use the appropriate registration form ONLY if you feel that you will need more time than the usual 3 weeks for submitting predictions. Predictions from the "extended timeframe" groups will be accepted for 6 weeks total. If the experimental structure becomes publicly available during the extended time window, the predictions accepted after that date will be discarded. Prediction Center does not fully control the extended deadlines and there is real risk that already submitted predictions will be discarded.
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| CASP8 update. New fold targets appeal. Refinement targets. | (2008-6-10) |
General participation statistics
We are in the middle of the CASP8 prediction season. Interest in the CASP experiments remains high. We have 221 groups including 121 servers actively participating in CASP8. More than 28 thousand predictions have been collected by the Prediction Center in the first 5 weeks of the experiment.
Targets
Fifty nine targets (including 28 human/server targets) have been released during the first part of the CASP8 experiment. As you may have noticed, there have so far been few small ‘new fold’ or very remote fold proteins suitable for testing non-template based modeling methods. This is starting to look like a problem, since, obviously, it's very important the community does find out how those methods are progressing.
So we are writing with an urgent appeal to help find target or targets of this type (typically 150 residues or less). Larger proteins with suitable semi-autonomous domains would also fill this need. For those, we need the relevant domain boundary information to be provided with the target. Please go and pester your friendly experimental colleagues, and see what you can come up with.
Refinement targets
The first target has been released for model refinement (TR389). The experimentalists kindly provided us with the coordinates for this target ahead of time. After the automatic evaluation of the models we want to suggest you one of the best models for refinement. Please, pay attention that the refinement target names start with "TR" instead of "T0" for regular targets.
CASP organizers
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| FORCASP migration | (2008-5-19) |
We are moving FORCASP discussion forum from the forcasp.org website to the predictioncenter.org site (link FORCASP forum is added to the menu). Old posts remain available at the forcasp.org website.
CASP organizers
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| Prediction in non-tertiary structure categories | (2008-5-16) |
Some targets in CASP8 Target List are marked as 'Human/server' and the others as 'Server only'. We have informed you that the human-expert groups should concentrate on predicting 3D structures for the Human/Server targets as the assessors will be comparing human-expert groups on this subset of targets. We want to clarify that this requirement pertains to the tertiary structure predictions only. Human-expert groups are expected to submit predictions for all targets (both "Human/Server" and "Server only") for the categories other than TS.
CASP8 organizers
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| Request for CASP8 targets | (2008-5-7) |
Dear CASP8 participants,
The CASP8 prediction experiment has just begun, and as always, it will only work if we have the help of the experimental community in providing targets.
Many targets have been provided by structural genomics centers in the last two CASPs, and expect to that will be the case again this time. However, we still very much need targets from the broader structural community. We need all sorts of targets but in particular, there are several sorts of targets we expect to be short of.
1. We expect the number of ‘new fold’ provided by the SG centers will be smaller this time, and we really really need these to test ‘ab iniito’ target prediction methods. So if you have one, we would be very very grateful if we could use it as target.
2. We want to improve our test set for assessing disorder prediction methods, so if you have structure that contains significant disorder, we would very much appreciate using it as a target.
3. In all the CASPs to date we have only ever had one membrane structure target, so if you have you could make available, that would be great.
CASP only succeeds because of the support and co-operation of the members of this community, and we very much need your help.
The time table is similar to other CASPs: The prediction season opened at the beginning of May, and will run until the end of July. We will release targets continuously throughout that period, as evenly spaced as possible, and hope to have about 100 targets altogether. Each target will be available for prediction for a period of three weeks, although in some cases we request a longer period to allow it to be used to test refinement methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed.
It’s fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the beginning of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December.
So, if you have any thing suitable, we would be most grateful if you would enter the data on the web form: http://www.predictioncenter.org/casp8/targets_submission.cgi
OK, that's about it. Please get in touch if you have any questions or concerns. Hoping for lots of targets....
CASP8 organizers
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| CASP8 started | (2008-5-5) |
We have released the first two CASP8 targets. Good luck everyone in predicting these and all the subsequent CASP8 targets.
Please, pay special attention to the column "Type" in the Target List. In the current CASP experiment we are planning on releasing between 50 and 60 targets to be evaluated in the human and server track and many more targets (depending on target availability) to be evaluated in the server-only track. Assessors will be comparing all participating predictor groups on the subset of Human/Server targets and, additionally, the server groups on all released targets. The human-expert groups should concentrate on predicting structures for the Human/Server targets. Those, wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation emphasis will be placed on the "Human/Server" targets. Subject to availability, we will give priority to releasing targets containing low homology domains in the Human/Server track.
Server predictions for all targets will be made publicly available immediately after acceptance by the CASP verification system. Receiving status of server predictions can be checked from the main CASP8 web page by following the link "Server Predictions." Please note that tarballs of all 3D models (with AL predictions already converted into coordinates) will be posted at the same place usually with one-day later. The electronic address of these tarballs will be sent to the quality assessment (QA) servers 4 days after the original target release. QA servers will have an extra 3 days to submit QA predictions.
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| CASP8 server dry run - April 28 | (2008-4-28) |
On April 28 we will have the last round of dry runs for the servers. Please get your servers ready.
The first CASP8 targets will be released on May 5.
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| CASP8 server rules | (2008-4-2) |
CHANGES relative to CASP7
There will be just minor changes to the rules for server participation in CASP.
According to the suggestions of CASP7 predictor meeting, in CASP8 we are extending the window for accepting server predictions. Servers will now have full three days to return the prediction. No additional time for corrections will be allotted but corrections will be accepted within the original 72 hour window.
Also, according to another recommendation of the CASP7 predictor meeting, we will have two different sets of targets for evaluation in the human-and-server track and in the server-only track. We plan to release as many targets as possible for evaluation in the server-only track and a subset of around 50 targets from among these for the human-and-server track.
For the servers participating in the model quality assessment category, we will be sending a link to the tarball of accepted server structure predictions on a particular target in 1 business day after closing the window for server 3D predictions. The quality assessment servers will have another 3 days to generate the model quality assessment prediction.
DRY RUN
We will be testing connectivity with registered CASP8 servers starting on April 14, 2008. To test your server, we will send you an old CASP7 target (T0283). Please respond as you would for CASP8 targets. Of course, these predictions will not be part of the CASP8 experiment.
If your server participated in CASP7, we expect the test to be just a formal recheck. For new servers: we will be sending 3 variables to your server's submission URL: the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results). For the quality assessment servers we will be sending the TARBALL-LOCATION variable instead of (or in addition to, if you specify so) the SEQUENCE. Please, make sure you provide the required parameters in your CASP8 server registration.
IMPORTANT THINGS TO REMEMBER
1. Target distribution procedure for servers.
You will be receiving CASP8 queries from the distribution server in Davis and the results will be collected directly by the Prediction Center. At the end of each week we will notify you about how many targets we plan to release the following week. Targets are planned to be released on business days only. We plan not to exceed a load of 3 targets per day for servers. Targets will be made available and requests to all servers will be sent around 9am PST. The submission engine will resend the query if it encounters obvious connecting problems (network timeouts, 'no response' etc.). Failures that go beyond that require special attention, but we'll make every effort to notify server curators ASAP if we suspect something is not working. The facility that allows checking data flow status by server predictors will also be available.
2. Server submission format.
Please submit your predictions in the standard CASP format. Your submissions will be immediately verified at time of submission. CASP warning and error messages will return directly and immediately to you, and will refer to the material you submitted, allowing you to respond in close to a server time frame, if necessary. Please note that, as in previous experiments, no prediction will be finally accepted by CASP until it passes CASP format verification.
Below we summarize differences in format of server submissions from that of human groups.
2.1 Header AUTHOR should contain your group name instead of the 12-digit predictor code, e.g.
AUTHOR 3D-JIGSAW
or
REMARK AUTHOR 3D-JIGSAW
2.2. Header SCORE in your prediction is allowable and optional (a real number reflecting self-estimation of the prediction quality).
2.3. For servers, it is allowed to have several models for the same target in one file. If your server returns only one file with several models, we will preprocess such an entry. You may add only one set of required header fields (PFRMAT, TARGET and AUTHOR) at the beginning of the file. Our script will split a multiple model file into separate files (one model per file) and only then we will send each model separately to our verification software (models numbered 6 and higher will be ignored). Error messages (if any) will be sent for each model separately. So you will be able to correct models (if needed) separately.
3. The timeframe for server prediction acceptance is the following. All server groups have 72 hours since target distribution to return the prediction. Error notifications will be sent to the server contact person's email address. If your prediction doesn't pass the CASP verification system, you will need to correct your format manually and resubmit the rejected prediction within the original 72-hour window. To do this, you will need to include the following line in your revised prediction:
REMARK Corrected server submission
and send it by email to: servers@predictioncenter.org .
After 72 hours no server predictions will be accepted or altered in any way. If you expect your server to work on prediction generation more than 72 hours, then we would advise you to register a regular (not server) prediction group for CASP8 instead.
You will be able to check the submission status of your prediction through the Server Submission Status Page or through the Model Viewer facility.
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| CASP8 registration | (2008-3-22) |
The registration for CASP8 experiment is now open.
To register for the experiment, you will need to register with the Prediction Center (PC) first (if you haven't done this yet). At this step we will collect the basic registration information to be used for your participation in CASP8, all subsequent CASP experiments, between-CASP initiatives, and local services. The information provided by you will not be shared with anyone outside of the CASP system.
After you register with PC and login to our website, you will be able to register for the CASP8 experiment (a separate registration form under the CASP8 menu). You will find five separate registration forms there. Please, read the registration instructions and use the appropriate form.
We ask that you register with the Prediction Center at your earliest opportunity as we plan to release future CASP8-related news mainly through our website. We recommend that you select an option "Subscribe for Prediction Center newsletters" as in this case you will be receiving emails every time the news are posted on our website. This functionality was just recently added to our registration form. So, if you have registered earlier, please go to "My personal Data" link and select this option.
Also, we ask server group leaders to register as soon as possible as we are planning on testing the connectivity with the registered CASP8 servers starting April 14, 2008. Server participation rules and the details of the dry run will be posted in the Message Board section of our website shortly (this section is available from both the Prediction Center home page and the CASP8 home page).
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| CASP8 preliminary timetable | (2008-2-1) |
Registration for the experiment will start in the last week of March 2008.
Prediction season will run from early May through early August 2008. The first prediction targets will be released not earlier than May 5, 2008; the last prediction targets will be released not later than July 18, 2008; prediction season will end not later than August 1, 2008.
According to the recommendations of the CASP7 predictors meeting, we will be releasing about 50 targets for evaluation in the human and server track and as many targets as we can for evaluation in the server-only track (including "human and server" targets). The human-expert groups wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation accent will be placed on the selected targets. Subject to the availability, we will give priority to targets containing low homology domains for inclusion in the human-expert modeling experiment.
The meeting to discuss results of the experiment will be held on the island of Sardinia, Italy, December 3-7, 2008. The meeting will take place at Hotel Setar , near Cagliari. The hotel is located in Quartu S. Elena, 10 kilometers from Cagliari and 15 from the Cagliari airport.
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| CASP 7.5 meeting | (2008-2-1) |
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Together with CNIO, Madrid, we are organizing the next between-CASP meeting (CASP7.5). It is going to take place in Madrid, Spain in April 2008. The idea of the between CASP meetings is to update the progress of structure prediction as measured by the CASP experiments. In contrast to the full CASP meetings that are exclusively for participants and developers, this meeting will be open to all interested scientists. All interested please check the meeting web page: http://ubio.bioinfo.cnio.es/casp/index.html
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| Opportunity to obtain the structure of a protein of interest in your research | (2008-1-1) |
Please share with your colleagues!
We are happy to announce an opportunity to obtain the three-dimensional structure of proteins you are working on. As part of the forthcoming CASP13 experiment, Dr. Gaetano Montelione and colleagues (http://www-nmr.cabm.rutgers.edu) will determine structures of a few proteins using NMR. Concurrently, these structures will be predicted as part of the CASP13 experiment.
We are seeking proteins for which knowledge of structure will significantly advance research programs, and invite your nominations.
There are some restrictions on proteins that will be considered, imposed by the need to test structure modeling methods, and the limited resources available for experimental structure determination:
No significant sequence homology to any of the structures in the PDB
60-180 amino acid residues, preferably monomeric domain
Predicted to be ordered (i.e. not an intrinsically disordered protein)
Soluble, non-disulfide bonded, globular protein which is predicted to fold inside of the cell
No integral membrane proteins will be pursued in this cycle
Shallow sequence alignment, avoiding high-accuracy evolutionary covariance contact prediction
Please provide a brief justification /explanation of your selection. Solved structures will be made publicly available.
Please submit your nominations to casp@predictioncenter.org with CASP NMR structure determination as subject line.
The CASP Organizing Committee and the Montelione Laboratory
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| End of CASP12 regular prediction season | (2008-1-1) |
*** Regular targets
Today we closed for prediction the last regular CASP12 target - T0946. All in all, we released 82 targets including 56 all-group targets, and collected over 53,000 predictions. The Prediction Center and the assessors already got access to many of the CASP12 structures and are in the process of evaluating the submitted models.
*** Refinement targets
The last refinement target was released today. All in all, we have released a record high 42 targets in this category (cf 37 in CASP11) . The latest deadline for the refinement targets is August 17.
*** SAXS-assisted targets
Ten targets have been released in this category so far. Data on an additional target is expected early next week. That will be the last SAXS-assisted target in the scope of CASP12 experiment. We want to take an opportunity here and thank to Greg Hura and Susan Tsutakawa from Lawrence Berkeley Lab, who did SAXS data acquisition for the selected CASP12 targets.
*** Cross-linking assisted targets
This is an important new direction (pioneered in CASP11) and we have tried to obtain cross linking data on at least some of the CASP12 targets. As target sample acquisition /data collection is time consuming, only today we are able to release data on the first set of these targets, the T0894/895 complex. We currently have prospects for cross linking datasets on approximately 10 additional proteins. We will be releasing these progressively, as soon as we have the experimental data in hand. We will inform you by email of every new release and implement longer prediction windows (3-4 weeks) to allow for more flexibility in modeling during the summer months. We will provide assessment for as many of these targets as we can as part of the CASP12 experiment. We are also looking into the options of providing experimental data and assessment on cross linking assisted targets in the future, if interest in this area is sufficient.
CASP organizers
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| Opportunity to obtain the structure of a protein of interest in your research | (2008-1-1) |
Please share with your colleagues!
We are happy to announce an opportunity to obtain the three-dimensional structure of proteins you are working on. As part of the forthcoming CASP13 experiment, Dr. Gaetano Montelione and colleagues (www-nmr.cabm.rutgers.edu) will determine structures of a few proteins using NMR. Concurrently, these structures will be predicted as part of the CASP13 experiment.
We are seeking proteins for which knowledge of structure will significantly advance research programs, and invite your nominations.
There are some restrictions on proteins that will be considered, imposed by the need to test structure modeling methods, and the limited resources available for experimental structure determination:
- No significant sequence homology to any of the structures in the PDB
- 60-180 amino acid residues, preferably monomeric domain
- Predicted to be ordered (i.e. not an intrinsically disordered protein)
- Soluble, non-disulfide bonded, globular protein which is predicted to fold inside of the cell
- No integral membrane proteins will be pursued in this cycle
- Shallow sequence alignment, avoiding high-accuracy evolutionary covariance contact prediction
Please provide a brief justification /explanation of your selection. Solved structures will be made publicly available.
Please submit your nominations to casp@predictioncenter.org with CASP NMR structure determination as subject line.
The CASP Organizing Committee and the Montelione Laboratory
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| CASP10 dry run for servers | (2008-1-1) |
Dear Caspers,
As of today, 72 prediction servers have been registered for CASP10 experiment. We have started checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. We have sent them 1-3 requests to predict the test target T0921. If you had registered a TS, RR, DR or FN server, but have not received at least one request from us - please check your registration settings and contact us if in doubt. Quality assessment servers will be tested starting tomorrow afternoon (PST). We also plan to send one more modeling request to all registered non-QA servers tomorrow morning (PST). So, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so immediately. During the tomorrow tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be suppressed.
A request to all EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0921 - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. The prediction itself should be sent to the address specified in the field REPLY-E-MAIL of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).
CASP organizers
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