
PFRMAT TS
TARGET T0348
AUTHOR SAM_T06_server
REMARK   6 
REMARK   6 T0348 model 5 Tue Jun 27 13:30:46 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    10      18.129   8.713  -1.693  1.00  0.00
ATOM      3  CA  VAL    10      18.756   9.452  -2.810  1.00  0.00
ATOM      4  CB  VAL    10      20.277   9.214  -2.860  1.00  0.00
ATOM      5  CG1 VAL    10      20.934   9.686  -1.571  1.00  0.00
ATOM      6  CG2 VAL    10      20.578   7.732  -3.037  1.00  0.00
ATOM      7  O   VAL    10      17.706   7.859  -4.203  1.00  0.00
ATOM      8  C   VAL    10      18.162   8.994  -4.094  1.00  0.00
ATOM      9  N   CYS    11      18.164   9.876  -5.077  1.00  0.00
ATOM     10  CA  CYS    11      17.568   9.574  -6.364  1.00  0.00
ATOM     11  CB  CYS    11      17.281  10.862  -7.137  1.00  0.00
ATOM     12  SG  CYS    11      16.552  10.606  -8.772  1.00  0.00
ATOM     13  O   CYS    11      19.685   9.113  -7.370  1.00  0.00
ATOM     14  C   CYS    11      18.553   8.705  -7.160  1.00  0.00
ATOM     15  N   PRO    12      18.134   7.529  -7.616  1.00  0.00
ATOM     16  CA  PRO    12      18.992   6.683  -8.444  1.00  0.00
ATOM     17  CB  PRO    12      18.181   5.399  -8.627  1.00  0.00
ATOM     18  CG  PRO    12      17.210   5.406  -7.495  1.00  0.00
ATOM     19  CD  PRO    12      16.892   6.850  -7.226  1.00  0.00
ATOM     20  O   PRO    12      20.366   6.893 -10.375  1.00  0.00
ATOM     21  C   PRO    12      19.350   7.268  -9.813  1.00  0.00
ATOM     22  N   LEU    13      18.517   8.173 -10.335  1.00  0.00
ATOM     23  CA  LEU    13      18.751   8.812 -11.627  1.00  0.00
ATOM     24  CB  LEU    13      17.456   9.421 -12.167  1.00  0.00
ATOM     25  CG  LEU    13      17.555  10.132 -13.519  1.00  0.00
ATOM     26  CD1 LEU    13      17.989   9.161 -14.606  1.00  0.00
ATOM     27  CD2 LEU    13      16.208  10.720 -13.916  1.00  0.00
ATOM     28  O   LEU    13      20.702   9.993 -12.351  1.00  0.00
ATOM     29  C   LEU    13      19.795   9.940 -11.525  1.00  0.00
ATOM     30  N   CYS    14      19.687  10.808 -10.518  1.00  0.00
ATOM     31  CA  CYS    14      20.497  12.025 -10.497  1.00  0.00
ATOM     32  CB  CYS    14      19.612  13.262 -10.670  1.00  0.00
ATOM     33  SG  CYS    14      18.581  13.648  -9.237  1.00  0.00
ATOM     34  O   CYS    14      22.096  13.147  -9.110  1.00  0.00
ATOM     35  C   CYS    14      21.270  12.213  -9.203  1.00  0.00
ATOM     36  N   LYS    15      21.013  11.367  -8.193  1.00  0.00
ATOM     37  CA  LYS    15      21.796  11.465  -6.953  1.00  0.00
ATOM     38  CB  LYS    15      23.240  11.865  -7.260  1.00  0.00
ATOM     39  CG  LYS    15      24.016  10.829  -8.058  1.00  0.00
ATOM     40  CD  LYS    15      25.442  11.285  -8.317  1.00  0.00
ATOM     41  CE  LYS    15      26.210  10.260  -9.135  1.00  0.00
ATOM     42  NZ  LYS    15      27.620  10.678  -9.368  1.00  0.00
ATOM     43  O   LYS    15      21.916  12.543  -4.794  1.00  0.00
ATOM     44  C   LYS    15      21.334  12.473  -5.894  1.00  0.00
ATOM     45  N   GLY    16      20.308  13.273  -6.191  1.00  0.00
ATOM     46  CA  GLY    16      19.817  14.227  -5.164  1.00  0.00
ATOM     47  O   GLY    16      18.491  12.403  -4.383  1.00  0.00
ATOM     48  C   GLY    16      18.910  13.534  -4.166  1.00  0.00
ATOM     49  N   PRO    17      18.596  14.220  -3.079  1.00  0.00
ATOM     50  CA  PRO    17      17.762  13.667  -2.031  1.00  0.00
ATOM     51  CB  PRO    17      17.913  14.660  -0.876  1.00  0.00
ATOM     52  CG  PRO    17      18.275  15.948  -1.535  1.00  0.00
ATOM     53  CD  PRO    17      19.094  15.583  -2.741  1.00  0.00
ATOM     54  O   PRO    17      15.876  14.421  -3.262  1.00  0.00
ATOM     55  C   PRO    17      16.330  13.568  -2.501  1.00  0.00
ATOM     56  N   LEU    18      15.635  12.506  -2.082  1.00  0.00
ATOM     57  CA  LEU    18      14.224  12.343  -2.391  1.00  0.00
ATOM     58  CB  LEU    18      13.928  10.896  -2.791  1.00  0.00
ATOM     59  CG  LEU    18      14.738  10.337  -3.962  1.00  0.00
ATOM     60  CD1 LEU    18      14.389   8.877  -4.209  1.00  0.00
ATOM     61  CD2 LEU    18      14.451  11.116  -5.235  1.00  0.00
ATOM     62  O   LEU    18      13.842  12.944  -0.072  1.00  0.00
ATOM     63  C   LEU    18      13.347  12.687  -1.200  1.00  0.00
ATOM     64  N   VAL    19      12.039  12.743  -1.460  1.00  0.00
ATOM     65  CA  VAL    19      11.081  12.973  -0.394  1.00  0.00
ATOM     66  CB  VAL    19      10.806  14.475  -0.197  1.00  0.00
ATOM     67  CG1 VAL    19      10.155  15.066  -1.438  1.00  0.00
ATOM     68  CG2 VAL    19       9.874  14.695   0.985  1.00  0.00
ATOM     69  O   VAL    19       9.562  12.072  -2.007  1.00  0.00
ATOM     70  C   VAL    19       9.805  12.257  -0.811  1.00  0.00
ATOM     71  N   PHE    20       9.001  11.833   0.166  1.00  0.00
ATOM     72  CA  PHE    20       7.825  10.991  -0.108  1.00  0.00
ATOM     73  CB  PHE    20       7.254  10.427   1.193  1.00  0.00
ATOM     74  CG  PHE    20       6.086   9.505   0.994  1.00  0.00
ATOM     75  CD1 PHE    20       6.280   8.201   0.570  1.00  0.00
ATOM     76  CD2 PHE    20       4.793   9.940   1.230  1.00  0.00
ATOM     77  CE1 PHE    20       5.204   7.352   0.386  1.00  0.00
ATOM     78  CE2 PHE    20       3.719   9.091   1.046  1.00  0.00
ATOM     79  CZ  PHE    20       3.920   7.802   0.626  1.00  0.00
ATOM     80  O   PHE    20       6.467  12.911  -0.421  1.00  0.00
ATOM     81  C   PHE    20       6.724  11.789  -0.801  1.00  0.00
ATOM     82  N   ASP    21       6.058  11.224  -1.804  1.00  0.00
ATOM     83  CA  ASP    21       4.855  11.874  -2.333  1.00  0.00
ATOM     84  CB  ASP    21       4.285  11.072  -3.506  1.00  0.00
ATOM     85  CG  ASP    21       5.128  11.194  -4.759  1.00  0.00
ATOM     86  OD1 ASP    21       6.044  12.042  -4.779  1.00  0.00
ATOM     87  OD2 ASP    21       4.871  10.442  -5.724  1.00  0.00
ATOM     88  O   ASP    21       3.654  11.099  -0.381  1.00  0.00
ATOM     89  C   ASP    21       3.769  11.983  -1.257  1.00  0.00
ATOM     90  N   LYS    22       2.971  13.041  -1.332  1.00  0.00
ATOM     91  CA  LYS    22       1.819  13.223  -0.434  1.00  0.00
ATOM     92  CB  LYS    22       1.576  14.710  -0.169  1.00  0.00
ATOM     93  CG  LYS    22       2.694  15.395   0.599  1.00  0.00
ATOM     94  CD  LYS    22       2.406  16.875   0.789  1.00  0.00
ATOM     95  CE  LYS    22       3.520  17.559   1.566  1.00  0.00
ATOM     96  NZ  LYS    22       3.238  19.004   1.784  1.00  0.00
ATOM     97  O   LYS    22      -0.469  12.493  -0.308  1.00  0.00
ATOM     98  C   LYS    22       0.526  12.638  -1.025  1.00  0.00
ATOM     99  N   SER    23       0.520  12.341  -2.332  1.00  0.00
ATOM    100  CA  SER    23      -0.718  11.911  -3.012  1.00  0.00
ATOM    101  CB  SER    23      -0.961  12.754  -4.266  1.00  0.00
ATOM    102  OG  SER    23       0.091  12.591  -5.200  1.00  0.00
ATOM    103  O   SER    23      -1.716   9.904  -3.867  1.00  0.00
ATOM    104  C   SER    23      -0.696  10.441  -3.461  1.00  0.00
ATOM    105  N   LYS    24       0.463   9.804  -3.377  1.00  0.00
ATOM    106  CA  LYS    24       0.641   8.423  -3.758  1.00  0.00
ATOM    107  CB  LYS    24       1.087   8.323  -5.218  1.00  0.00
ATOM    108  CG  LYS    24       0.099   8.911  -6.211  1.00  0.00
ATOM    109  CD  LYS    24       0.613   8.796  -7.636  1.00  0.00
ATOM    110  CE  LYS    24      -0.413   9.301  -8.637  1.00  0.00
ATOM    111  NZ  LYS    24       0.052   9.134 -10.042  1.00  0.00
ATOM    112  O   LYS    24       2.449   8.591  -2.204  1.00  0.00
ATOM    113  C   LYS    24       1.698   7.855  -2.844  1.00  0.00
ATOM    114  N   ASP    25       1.792   6.539  -2.835  1.00  0.00
ATOM    115  CA  ASP    25       2.875   5.856  -2.167  1.00  0.00
ATOM    116  CB  ASP    25       2.455   4.437  -1.782  1.00  0.00
ATOM    117  CG  ASP    25       3.495   3.731  -0.932  1.00  0.00
ATOM    118  OD1 ASP    25       4.504   4.376  -0.573  1.00  0.00
ATOM    119  OD2 ASP    25       3.302   2.537  -0.625  1.00  0.00
ATOM    120  O   ASP    25       4.270   4.832  -3.889  1.00  0.00
ATOM    121  C   ASP    25       4.064   5.805  -3.150  1.00  0.00
ATOM    122  N   GLU    26       4.791   6.919  -3.192  1.00  0.00
ATOM    123  CA  GLU    26       5.849   7.114  -4.135  1.00  0.00
ATOM    124  CB  GLU    26       5.321   7.800  -5.396  1.00  0.00
ATOM    125  CG  GLU    26       4.236   7.018  -6.119  1.00  0.00
ATOM    126  CD  GLU    26       3.694   7.756  -7.329  1.00  0.00
ATOM    127  OE1 GLU    26       4.163   8.883  -7.596  1.00  0.00
ATOM    128  OE2 GLU    26       2.801   7.208  -8.008  1.00  0.00
ATOM    129  O   GLU    26       6.680   8.596  -2.440  1.00  0.00
ATOM    130  C   GLU    26       6.901   7.986  -3.479  1.00  0.00
ATOM    131  N   LEU    27       8.077   7.959  -4.074  1.00  0.00
ATOM    132  CA  LEU    27       9.181   8.753  -3.662  1.00  0.00
ATOM    133  CB  LEU    27      10.396   7.872  -3.367  1.00  0.00
ATOM    134  CG  LEU    27      10.227   6.833  -2.257  1.00  0.00
ATOM    135  CD1 LEU    27      11.455   5.943  -2.160  1.00  0.00
ATOM    136  CD2 LEU    27      10.023   7.512  -0.912  1.00  0.00
ATOM    137  O   LEU    27       9.601   9.273  -5.982  1.00  0.00
ATOM    138  C   LEU    27       9.471   9.719  -4.849  1.00  0.00
ATOM    139  N   ILE    28       9.520  11.020  -4.562  1.00  0.00
ATOM    140  CA  ILE    28       9.752  12.089  -5.540  1.00  0.00
ATOM    141  CB  ILE    28       8.706  13.209  -5.410  1.00  0.00
ATOM    142  CG1 ILE    28       8.769  13.841  -4.017  1.00  0.00
ATOM    143  CG2 ILE    28       7.305  12.659  -5.626  1.00  0.00
ATOM    144  CD1 ILE    28       7.912  15.079  -3.868  1.00  0.00
ATOM    145  O   ILE    28      11.690  12.630  -4.214  1.00  0.00
ATOM    146  C   ILE    28      11.138  12.697  -5.320  1.00  0.00
ATOM    147  N   CYS    29      11.675  13.308  -6.368  1.00  0.00
ATOM    148  CA  CYS    29      13.027  13.823  -6.348  1.00  0.00
ATOM    149  CB  CYS    29      13.715  13.578  -7.691  1.00  0.00
ATOM    150  SG  CYS    29      15.428  14.151  -7.771  1.00  0.00
ATOM    151  O   CYS    29      12.182  16.011  -6.649  1.00  0.00
ATOM    152  C   CYS    29      13.001  15.310  -6.078  1.00  0.00
ATOM    153  N   LYS    30      13.902  15.793  -5.219  1.00  0.00
ATOM    154  CA  LYS    30      14.001  17.213  -4.938  1.00  0.00
ATOM    155  CB  LYS    30      14.935  17.461  -3.751  1.00  0.00
ATOM    156  CG  LYS    30      14.390  16.968  -2.421  1.00  0.00
ATOM    157  CD  LYS    30      15.379  17.217  -1.293  1.00  0.00
ATOM    158  CE  LYS    30      14.820  16.756   0.043  1.00  0.00
ATOM    159  NZ  LYS    30      15.785  16.980   1.155  1.00  0.00
ATOM    160  O   LYS    30      14.392  19.192  -6.146  1.00  0.00
ATOM    161  C   LYS    30      14.543  17.985  -6.113  1.00  0.00
ATOM    162  N   GLY    31      15.165  17.300  -7.072  1.00  0.00
ATOM    163  CA  GLY    31      15.852  17.962  -8.203  1.00  0.00
ATOM    164  O   GLY    31      14.937  18.533 -10.355  1.00  0.00
ATOM    165  C   GLY    31      15.245  17.635  -9.569  1.00  0.00
ATOM    166  N   ASP    32      15.068  16.354  -9.865  1.00  0.00
ATOM    167  CA  ASP    32      14.601  15.966 -11.181  1.00  0.00
ATOM    168  CB  ASP    32      15.405  14.774 -11.703  1.00  0.00
ATOM    169  CG  ASP    32      16.835  15.141 -12.049  1.00  0.00
ATOM    170  OD1 ASP    32      17.126  16.351 -12.160  1.00  0.00
ATOM    171  OD2 ASP    32      17.664  14.221 -12.207  1.00  0.00
ATOM    172  O   ASP    32      12.427  15.649 -10.103  1.00  0.00
ATOM    173  C   ASP    32      13.122  15.564 -11.142  1.00  0.00
ATOM    174  N   ARG    33      12.660  15.080 -12.283  1.00  0.00
ATOM    175  CA  ARG    33      11.258  14.748 -12.479  1.00  0.00
ATOM    176  CB  ARG    33      10.815  15.109 -13.899  1.00  0.00
ATOM    177  CG  ARG    33      10.859  16.599 -14.203  1.00  0.00
ATOM    178  CD  ARG    33      10.327  16.895 -15.595  1.00  0.00
ATOM    179  NE  ARG    33      10.386  18.319 -15.913  1.00  0.00
ATOM    180  CZ  ARG    33      10.059  18.836 -17.093  1.00  0.00
ATOM    181  NH1 ARG    33      10.145  20.144 -17.291  1.00  0.00
ATOM    182  NH2 ARG    33       9.647  18.043 -18.073  1.00  0.00
ATOM    183  O   ARG    33       9.767  12.877 -12.376  1.00  0.00
ATOM    184  C   ARG    33      10.928  13.266 -12.288  1.00  0.00
ATOM    185  N   LEU    34      11.938  12.438 -11.998  1.00  0.00
ATOM    186  CA  LEU    34      11.685  10.995 -11.888  1.00  0.00
ATOM    187  CB  LEU    34      12.988  10.209 -12.050  1.00  0.00
ATOM    188  CG  LEU    34      13.698  10.344 -13.397  1.00  0.00
ATOM    189  CD1 LEU    34      15.024   9.598 -13.383  1.00  0.00
ATOM    190  CD2 LEU    34      12.842   9.770 -14.516  1.00  0.00
ATOM    191  O   LEU    34      11.085  11.436  -9.552  1.00  0.00
ATOM    192  C   LEU    34      11.080  10.632 -10.521  1.00  0.00
ATOM    193  N   ALA    35      10.532   9.425 -10.447  1.00  0.00
ATOM    194  CA  ALA    35       9.924   8.977  -9.205  1.00  0.00
ATOM    195  CB  ALA    35       8.478   9.439  -9.126  1.00  0.00
ATOM    196  O   ALA    35      10.212   6.783 -10.125  1.00  0.00
ATOM    197  C   ALA    35       9.956   7.437  -9.124  1.00  0.00
ATOM    198  N   PHE    36       9.772   6.894  -7.917  1.00  0.00
ATOM    199  CA  PHE    36       9.818   5.453  -7.670  1.00  0.00
ATOM    200  CB  PHE    36      11.038   5.094  -6.819  1.00  0.00
ATOM    201  CG  PHE    36      12.351   5.427  -7.468  1.00  0.00
ATOM    202  CD1 PHE    36      12.969   6.642  -7.228  1.00  0.00
ATOM    203  CD2 PHE    36      12.966   4.527  -8.320  1.00  0.00
ATOM    204  CE1 PHE    36      14.176   6.949  -7.826  1.00  0.00
ATOM    205  CE2 PHE    36      14.173   4.833  -8.918  1.00  0.00
ATOM    206  CZ  PHE    36      14.779   6.039  -8.674  1.00  0.00
ATOM    207  O   PHE    36       8.034   5.760  -6.123  1.00  0.00
ATOM    208  C   PHE    36       8.572   5.012  -6.939  1.00  0.00
ATOM    209  N   PRO    37       8.135   3.787  -7.231  1.00  0.00
ATOM    210  CA  PRO    37       6.966   3.176  -6.593  1.00  0.00
ATOM    211  CB  PRO    37       5.999   2.930  -7.752  1.00  0.00
ATOM    212  CG  PRO    37       6.881   2.624  -8.916  1.00  0.00
ATOM    213  CD  PRO    37       8.112   3.468  -8.738  1.00  0.00
ATOM    214  O   PRO    37       8.327   1.240  -6.384  1.00  0.00
ATOM    215  C   PRO    37       7.392   1.882  -5.909  1.00  0.00
TER
END



