
PFRMAT TS
TARGET T0358
AUTHOR SAM_T06_server
REMARK   6 
REMARK   6 T0358 model 5 Wed Jul  5 16:13:40 2006
METHOD The SAM-T06 server uses methods similar to SAM_T04 in CASP6 and
METHOD the SAM-T02 method in CASP5.
METHOD 
METHOD We start with a fully automated method:
METHOD    
METHOD     Use the SAM-T2K and SAM-T04 methods for finding homologs of the
METHOD       target and aligning them.
METHOD 
METHOD     Make local structure predictions using neural nets and the
METHOD       multiple alignments.  Different neural nets are used for the
METHOD       SAM-T2K alignments and the SAM-T04 alignments.
METHOD       We currently use 8 local-structure alphabets: 
METHOD 	DSSP
METHOD 	STRIDE
METHOD 	STR2	an extended version of DSSP that splits the beta strands
METHOD 		into multiple classes (parallel/antiparallel/mixed,
METHOD 					edge/center)
METHOD 	ALPHA	an discretization of the alpha torsion angle:
METHOD 		CA(i-i), CA(i), CA(i+1), CA(i+2)
METHOD 	BYS	a discretization of Ramachandran plots, due to Bystroff
METHOD 	CB_burial_14_7	a 7-state discretization of the number of C_beta
METHOD 		atoms in a 14 Angstrom radius sphere around the C_beta.
METHOD 	near-backbone-11 an 11-state discretization of the number of
METHOD 	      residues (represented by near-backbone points) in a 
METHOD 	      9.65 Angstrom radius sphere around the sidechain proxy
METHOD 	      spot for the residue.
METHOD 	DSSP_EHL2	CASP's collapse of the DSSP alphabet
METHOD 			DSSP_EHL2 is not predicted directly by a
METHOD 			neural net, but is computed as a weighted
METHOD 			average of the other backbone alphabet predictions. 
METHOD     
METHOD     We make 2-track HMMs with each alphabet (1.0 amino acid + 0.3 local structure)
METHOD       and use them to score a template library of 6400 (t04) or 9900 (t2k) templates
METHOD       We also used a single-track HMM to score not just the template
METHOD       library, but a non-redundant copy of the entire PDB.
METHOD 
METHOD     We also made a few 3-track HMMs (AA, str2, CB_burial_14_7 and 
METHOD       AA, str2, near-backbone-11) for finding and aligning more remote
METHOD       homologs.
METHOD     
METHOD     One-track HMMs built from the template library multiple alignments
METHOD        were used to score the target sequence (for early targets, only
METHOD        t2k template library was searched this way).
METHOD 
METHOD     All the logs of e-values were combined in a weighted average (with
METHOD        rather arbitrary weights, since we did not have time to
METHOD        optimize them), and the best templates ranked.  Ranking was
METHOD        separate for predictions from the t2k and t04 multiple alignments.
METHOD     
METHOD     Alignments of the target to the top templates were made using
METHOD       several different alignment methods (mainly using the SAM hmmscore
METHOD       program, but a few alignments were made with Bob Edgar's MUSCLE
METHOD       profile-profile aligner).
METHOD 
METHOD     Generate fragments (short 9-residue alignments for each position)
METHOD       using SAM's "fragfinder" program and the 3-track HMM.
METHOD 
METHOD     Then the "undertaker" program (named because it optimizes burial)
METHOD       is used to try to combine the alignments and the fragments into
METHOD       a consistent 3D model.  No single alignment or parent template
METHOD       was used, though in many cases one had much more influence than
METHOD       the others.  The alignment scores were not passed to undertaker,
METHOD       but were used only to pick the set of alignments and fragments
METHOD       that undertaker would see.  Helix and strand constraints
METHOD       generated from the secondary-structure predictions are passed to
METHOD       undertaker to use in the cost function.
METHOD 
METHOD     One important change in this server over previous methods is that
METHOD     sheet constraints are extracted from the top few alignments and
METHOD     passed to undertaker. 
METHOD -------------
MODEL  5
PARENT N/A
ATOM      2  N   VAL    40      -4.791  13.442  14.726  1.00  0.00
ATOM      3  CA  VAL    40      -5.672  12.782  13.747  1.00  0.00
ATOM      4  CB  VAL    40      -5.330  11.287  13.599  1.00  0.00
ATOM      5  CG1 VAL    40      -6.370  10.586  12.739  1.00  0.00
ATOM      6  CG2 VAL    40      -3.969  11.114  12.941  1.00  0.00
ATOM      7  O   VAL    40      -7.966  13.415  13.467  1.00  0.00
ATOM      8  C   VAL    40      -7.117  12.897  14.194  1.00  0.00
ATOM      9  N   VAL    41      -7.375  12.466  15.417  1.00  0.00
ATOM     10  CA  VAL    41      -8.724  12.483  15.969  1.00  0.00
ATOM     11  CB  VAL    41      -8.751  11.941  17.410  1.00  0.00
ATOM     12  CG1 VAL    41      -8.273  10.498  17.446  1.00  0.00
ATOM     13  CG2 VAL    41      -7.846  12.770  18.309  1.00  0.00
ATOM     14  O   VAL    41     -10.575  14.062  16.061  1.00  0.00
ATOM     15  C   VAL    41      -9.346  13.889  16.026  1.00  0.00
ATOM     16  N   ARG    42      -8.474  14.889  16.028  1.00  0.00
ATOM     17  CA  ARG    42      -8.824  16.282  16.200  1.00  0.00
ATOM     18  CB  ARG    42      -7.720  17.024  16.955  1.00  0.00
ATOM     19  CG  ARG    42      -7.515  16.544  18.382  1.00  0.00
ATOM     20  CD  ARG    42      -6.394  17.310  19.067  1.00  0.00
ATOM     21  NE  ARG    42      -6.170  16.848  20.435  1.00  0.00
ATOM     22  CZ  ARG    42      -5.119  17.182  21.174  1.00  0.00
ATOM     23  NH1 ARG    42      -4.998  16.714  22.409  1.00  0.00
ATOM     24  NH2 ARG    42      -4.187  17.985  20.677  1.00  0.00
ATOM     25  O   ARG    42      -9.599  18.056  14.747  1.00  0.00
ATOM     26  C   ARG    42      -9.022  16.967  14.838  1.00  0.00
ATOM     27  N   ASP    43      -8.524  16.336  13.779  1.00  0.00
ATOM     28  CA  ASP    43      -8.435  16.983  12.463  1.00  0.00
ATOM     29  CB  ASP    43      -7.338  16.331  11.618  1.00  0.00
ATOM     30  CG  ASP    43      -5.945  16.691  12.096  1.00  0.00
ATOM     31  OD1 ASP    43      -5.818  17.632  12.906  1.00  0.00
ATOM     32  OD2 ASP    43      -4.979  16.031  11.659  1.00  0.00
ATOM     33  O   ASP    43     -10.694  16.270  12.019  1.00  0.00
ATOM     34  C   ASP    43      -9.718  16.913  11.630  1.00  0.00
ATOM     35  N   GLU    45      -9.689  17.586  10.481  1.00  0.00
ATOM     36  CA  GLU    45     -10.760  17.496   9.486  1.00  0.00
ATOM     37  CB  GLU    45     -10.775  18.744   8.601  1.00  0.00
ATOM     38  CG  GLU    45     -11.174  20.018   9.329  1.00  0.00
ATOM     39  CD  GLU    45     -11.057  21.250   8.456  1.00  0.00
ATOM     40  OE1 GLU    45     -10.628  21.114   7.290  1.00  0.00
ATOM     41  OE2 GLU    45     -11.394  22.352   8.935  1.00  0.00
ATOM     42  O   GLU    45     -11.415  16.041   7.676  1.00  0.00
ATOM     43  C   GLU    45     -10.592  16.274   8.563  1.00  0.00
ATOM     44  N   GLY    46      -9.534  15.493   8.803  1.00  0.00
ATOM     45  CA  GLY    46      -9.098  14.418   7.915  1.00  0.00
ATOM     46  O   GLY    46      -7.964  16.131   6.677  1.00  0.00
ATOM     47  C   GLY    46      -8.371  14.967   6.692  1.00  0.00
ATOM     48  N   ARG    47      -8.215  14.145   5.651  1.00  0.00
ATOM     49  CA  ARG    47      -7.713  14.644   4.381  1.00  0.00
ATOM     50  CB  ARG    47      -7.839  16.166   4.317  1.00  0.00
ATOM     51  CG  ARG    47      -9.272  16.671   4.273  1.00  0.00
ATOM     52  CD  ARG    47      -9.322  18.189   4.230  1.00  0.00
ATOM     53  NE  ARG    47     -10.694  18.691   4.222  1.00  0.00
ATOM     54  CZ  ARG    47     -11.019  19.980   4.244  1.00  0.00
ATOM     55  NH1 ARG    47     -12.293  20.344   4.234  1.00  0.00
ATOM     56  NH2 ARG    47     -10.065  20.903   4.276  1.00  0.00
ATOM     57  O   ARG    47      -5.781  14.776   3.026  1.00  0.00
ATOM     58  C   ARG    47      -6.264  14.349   4.067  1.00  0.00
ATOM     62  N   TRP    50      -1.882   9.099   6.443  1.00  0.00
ATOM     63  CA  TRP    50      -1.124   8.788   7.659  1.00  0.00
ATOM     64  CB  TRP    50      -2.070   8.578   8.843  1.00  0.00
ATOM     65  CG  TRP    50      -1.366   8.319  10.137  1.00  0.00
ATOM     66  CD1 TRP    50      -1.182   7.109  10.743  1.00  0.00
ATOM     67  CD2 TRP    50      -0.746   9.293  10.987  1.00  0.00
ATOM     68  CE2 TRP    50      -0.208   8.601  12.091  1.00  0.00
ATOM     69  CE3 TRP    50      -0.594  10.681  10.924  1.00  0.00
ATOM     70  NE1 TRP    50      -0.487   7.267  11.918  1.00  0.00
ATOM     71  CZ2 TRP    50       0.470   9.249  13.121  1.00  0.00
ATOM     72  CZ3 TRP    50       0.079  11.321  11.948  1.00  0.00
ATOM     73  CH2 TRP    50       0.604  10.608  13.033  1.00  0.00
ATOM     74  O   TRP    50      -0.850   6.406   7.472  1.00  0.00
ATOM     75  C   TRP    50      -0.316   7.514   7.436  1.00  0.00
ATOM     76  N   ARG    51       0.983   7.680   7.229  1.00  0.00
ATOM     77  CA  ARG    51       1.893   6.574   7.030  1.00  0.00
ATOM     78  CB  ARG    51       3.152   7.041   6.298  1.00  0.00
ATOM     79  CG  ARG    51       2.906   7.498   4.869  1.00  0.00
ATOM     80  CD  ARG    51       4.177   8.039   4.235  1.00  0.00
ATOM     81  NE  ARG    51       4.585   9.310   4.828  1.00  0.00
ATOM     82  CZ  ARG    51       5.768   9.882   4.624  1.00  0.00
ATOM     83  NH1 ARG    51       6.050  11.041   5.205  1.00  0.00
ATOM     84  NH2 ARG    51       6.663   9.297   3.843  1.00  0.00
ATOM     85  O   ARG    51       2.629   6.796   9.315  1.00  0.00
ATOM     86  C   ARG    51       2.263   6.029   8.418  1.00  0.00
ATOM     87  N   ALA    52       2.143   4.718   8.606  1.00  0.00
ATOM     88  CA  ALA    52       2.349   4.113   9.924  1.00  0.00
ATOM     89  CB  ALA    52       1.034   3.583  10.476  1.00  0.00
ATOM     90  O   ALA    52       3.313   2.213   8.854  1.00  0.00
ATOM     91  C   ALA    52       3.333   2.958   9.828  1.00  0.00
ATOM     95  N   PHE    55       3.047  -2.289  13.342  1.00  0.00
ATOM     96  CA  PHE    55       2.131  -2.500  14.454  1.00  0.00
ATOM     97  CB  PHE    55       2.893  -2.519  15.781  1.00  0.00
ATOM     98  CG  PHE    55       2.010  -2.691  16.984  1.00  0.00
ATOM     99  CD1 PHE    55       1.532  -3.940  17.337  1.00  0.00
ATOM    100  CD2 PHE    55       1.658  -1.603  17.764  1.00  0.00
ATOM    101  CE1 PHE    55       0.720  -4.100  18.444  1.00  0.00
ATOM    102  CE2 PHE    55       0.846  -1.761  18.871  1.00  0.00
ATOM    103  CZ  PHE    55       0.378  -3.003  19.211  1.00  0.00
ATOM    104  O   PHE    55      -0.136  -1.720  14.609  1.00  0.00
ATOM    105  C   PHE    55       1.056  -1.413  14.574  1.00  0.00
ATOM    106  N   GLU    56       1.491  -0.157  14.608  1.00  0.00
ATOM    107  CA  GLU    56       0.612   1.002  14.613  1.00  0.00
ATOM    108  CB  GLU    56       1.428   2.295  14.529  1.00  0.00
ATOM    109  CG  GLU    56       0.593   3.562  14.587  1.00  0.00
ATOM    110  CD  GLU    56       1.440   4.820  14.565  1.00  0.00
ATOM    111  OE1 GLU    56       2.682   4.699  14.528  1.00  0.00
ATOM    112  OE2 GLU    56       0.860   5.926  14.585  1.00  0.00
ATOM    113  O   GLU    56      -1.517   1.323  13.592  1.00  0.00
ATOM    114  C   GLU    56      -0.355   0.988  13.432  1.00  0.00
ATOM    115  N   PRO    57       0.140   0.628  12.247  1.00  0.00
ATOM    116  CA  PRO    57      -0.681   0.579  11.028  1.00  0.00
ATOM    117  CB  PRO    57       0.331   0.320   9.909  1.00  0.00
ATOM    118  CG  PRO    57       1.514  -0.264  10.605  1.00  0.00
ATOM    119  CD  PRO    57       1.542   0.357  11.974  1.00  0.00
ATOM    120  O   PRO    57      -2.825  -0.359  10.657  1.00  0.00
ATOM    121  C   PRO    57      -1.713  -0.531  11.113  1.00  0.00
ATOM    122  N   ASP    58      -1.343  -1.662  11.715  1.00  0.00
ATOM    123  CA  ASP    58      -2.281  -2.759  11.952  1.00  0.00
ATOM    124  CB  ASP    58      -1.587  -3.911  12.680  1.00  0.00
ATOM    125  CG  ASP    58      -2.441  -5.163  12.738  1.00  0.00
ATOM    126  OD1 ASP    58      -3.520  -5.175  12.109  1.00  0.00
ATOM    127  OD2 ASP    58      -2.029  -6.132  13.411  1.00  0.00
ATOM    128  O   ASP    58      -4.601  -2.364  12.440  1.00  0.00
ATOM    129  C   ASP    58      -3.438  -2.241  12.813  1.00  0.00
TER
END



