
PFRMAT TS
TARGET T0348
AUTHOR SAM_T06_server
REMARK   6 
REMARK   6 T0348 model 4 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  4
PARENT N/A
ATOM      2  N   CYS    11      18.993   9.589  -5.088  1.00  0.00
ATOM      3  CA  CYS    11      18.845   9.437  -6.530  1.00  0.00
ATOM      4  CB  CYS    11      18.320  10.733  -7.154  1.00  0.00
ATOM      5  SG  CYS    11      16.603  11.118  -6.741  1.00  0.00
ATOM      6  O   CYS    11      21.199   9.748  -6.896  1.00  0.00
ATOM      7  C   CYS    11      20.191   9.102  -7.178  1.00  0.00
ATOM      8  N   PRO    12      20.225   8.083  -8.057  1.00  0.00
ATOM      9  CA  PRO    12      21.459   7.671  -8.737  1.00  0.00
ATOM     10  CB  PRO    12      21.001   6.571  -9.699  1.00  0.00
ATOM     11  CG  PRO    12      19.794   5.984  -9.047  1.00  0.00
ATOM     12  CD  PRO    12      19.059   7.134  -8.419  1.00  0.00
ATOM     13  O   PRO    12      23.344   8.919  -9.542  1.00  0.00
ATOM     14  C   PRO    12      22.118   8.814  -9.497  1.00  0.00
ATOM     15  N   LEU    13      21.298   9.667 -10.097  1.00  0.00
ATOM     16  CA  LEU    13      21.801  10.802 -10.864  1.00  0.00
ATOM     17  CB  LEU    13      21.004  10.970 -12.160  1.00  0.00
ATOM     18  CG  LEU    13      21.046   9.793 -13.139  1.00  0.00
ATOM     19  CD1 LEU    13      20.139  10.053 -14.331  1.00  0.00
ATOM     20  CD2 LEU    13      22.460   9.574 -13.655  1.00  0.00
ATOM     21  O   LEU    13      21.874  13.191 -10.634  1.00  0.00
ATOM     22  C   LEU    13      21.693  12.109 -10.078  1.00  0.00
ATOM     23  N   CYS    14      21.399  12.007  -8.784  1.00  0.00
ATOM     24  CA  CYS    14      21.276  13.190  -7.938  1.00  0.00
ATOM     25  CB  CYS    14      19.851  13.745  -7.998  1.00  0.00
ATOM     26  SG  CYS    14      19.645  15.358  -7.208  1.00  0.00
ATOM     27  O   CYS    14      20.706  12.508  -5.707  1.00  0.00
ATOM     28  C   CYS    14      21.595  12.856  -6.482  1.00  0.00
ATOM     29  N   LYS    15      22.973  14.990  -4.085  1.00  0.00
ATOM     30  CA  LYS    15      22.543  16.086  -3.226  1.00  0.00
ATOM     31  CB  LYS    15      22.937  17.432  -3.836  1.00  0.00
ATOM     32  CG  LYS    15      24.432  17.709  -3.814  1.00  0.00
ATOM     33  CD  LYS    15      24.752  19.060  -4.432  1.00  0.00
ATOM     34  CE  LYS    15      26.248  19.326  -4.434  1.00  0.00
ATOM     35  NZ  LYS    15      26.581  20.634  -5.066  1.00  0.00
ATOM     36  O   LYS    15      20.519  16.347  -1.960  1.00  0.00
ATOM     37  C   LYS    15      21.029  16.069  -3.045  1.00  0.00
ATOM     38  N   GLY    16      20.315  15.740  -4.118  1.00  0.00
ATOM     39  CA  GLY    16      18.858  15.686  -4.079  1.00  0.00
ATOM     40  O   GLY    16      18.704  13.325  -4.480  1.00  0.00
ATOM     41  C   GLY    16      18.375  14.274  -3.770  1.00  0.00
ATOM     42  N   PRO    17      17.593  14.142  -2.704  1.00  0.00
ATOM     43  CA  PRO    17      17.066  12.844  -2.303  1.00  0.00
ATOM     44  CB  PRO    17      17.277  12.813  -0.788  1.00  0.00
ATOM     45  CG  PRO    17      17.178  14.240  -0.367  1.00  0.00
ATOM     46  CD  PRO    17      17.621  15.055  -1.550  1.00  0.00
ATOM     47  O   PRO    17      14.800  13.623  -2.426  1.00  0.00
ATOM     48  C   PRO    17      15.591  12.710  -2.660  1.00  0.00
ATOM     49  N   LEU    18      15.229  11.564  -3.227  1.00  0.00
ATOM     50  CA  LEU    18      13.845  11.307  -3.612  1.00  0.00
ATOM     51  CB  LEU    18      13.708   9.910  -4.220  1.00  0.00
ATOM     52  CG  LEU    18      14.452   9.666  -5.535  1.00  0.00
ATOM     53  CD1 LEU    18      14.360   8.204  -5.943  1.00  0.00
ATOM     54  CD2 LEU    18      13.860  10.511  -6.653  1.00  0.00
ATOM     55  O   LEU    18      12.997  10.566  -1.493  1.00  0.00
ATOM     56  C   LEU    18      12.924  11.396  -2.399  1.00  0.00
ATOM     57  N   VAL    19      12.060  12.406  -2.383  1.00  0.00
ATOM     58  CA  VAL    19      11.130  12.595  -1.277  1.00  0.00
ATOM     59  CB  VAL    19      10.519  14.009  -1.289  1.00  0.00
ATOM     60  CG1 VAL    19      11.611  15.061  -1.174  1.00  0.00
ATOM     61  CG2 VAL    19       9.756  14.248  -2.583  1.00  0.00
ATOM     62  O   VAL    19       9.693  11.060  -2.424  1.00  0.00
ATOM     63  C   VAL    19       9.986  11.594  -1.356  1.00  0.00
ATOM     64  N   PHE    20       9.342  11.341  -0.222  1.00  0.00
ATOM     65  CA  PHE    20       8.229  10.400  -0.170  1.00  0.00
ATOM     66  CB  PHE    20       8.571   9.215   0.734  1.00  0.00
ATOM     67  CG  PHE    20       8.786   9.591   2.172  1.00  0.00
ATOM     68  CD1 PHE    20       7.728   9.602   3.065  1.00  0.00
ATOM     69  CD2 PHE    20      10.044   9.936   2.632  1.00  0.00
ATOM     70  CE1 PHE    20       7.925   9.949   4.388  1.00  0.00
ATOM     71  CE2 PHE    20      10.243  10.283   3.955  1.00  0.00
ATOM     72  CZ  PHE    20       9.189  10.289   4.833  1.00  0.00
ATOM     73  O   PHE    20       7.045  11.931   1.251  1.00  0.00
ATOM     74  C   PHE    20       6.972  11.068   0.376  1.00  0.00
ATOM     75  N   ASP    21       5.818  10.660  -0.142  1.00  0.00
ATOM     76  CA  ASP    21       4.543  11.217   0.294  1.00  0.00
ATOM     77  CB  ASP    21       3.469  10.991  -0.771  1.00  0.00
ATOM     78  CG  ASP    21       3.760  11.732  -2.061  1.00  0.00
ATOM     79  OD1 ASP    21       4.152  12.917  -1.989  1.00  0.00
ATOM     80  OD2 ASP    21       3.600  11.130  -3.142  1.00  0.00
ATOM     81  O   ASP    21       4.860   9.905   2.280  1.00  0.00
ATOM     82  C   ASP    21       4.078  10.557   1.590  1.00  0.00
ATOM     83  N   LYS    22       2.801  10.735   1.917  1.00  0.00
ATOM     84  CA  LYS    22       2.236  10.160   3.131  1.00  0.00
ATOM     85  CB  LYS    22       1.159  11.079   3.710  1.00  0.00
ATOM     86  CG  LYS    22       1.684  12.420   4.198  1.00  0.00
ATOM     87  CD  LYS    22       0.572  13.263   4.800  1.00  0.00
ATOM     88  CE  LYS    22       1.093  14.614   5.264  1.00  0.00
ATOM     89  NZ  LYS    22       0.007  15.463   5.828  1.00  0.00
ATOM     90  O   LYS    22       1.554   7.935   3.723  1.00  0.00
ATOM     91  C   LYS    22       1.599   8.802   2.849  1.00  0.00
ATOM     92  N   SER    23       1.109   8.623   1.624  1.00  0.00
ATOM     93  CA  SER    23       0.478   7.376   1.218  1.00  0.00
ATOM     94  CB  SER    23      -0.614   6.977   2.212  1.00  0.00
ATOM     95  OG  SER    23      -1.275   5.796   1.797  1.00  0.00
ATOM     96  O   SER    23      -1.012   8.383  -0.376  1.00  0.00
ATOM     97  C   SER    23      -0.155   7.526  -0.158  1.00  0.00
ATOM     98  N   LYS    24       0.278   6.683  -1.080  1.00  0.00
ATOM     99  CA  LYS    24      -0.229   6.696  -2.450  1.00  0.00
ATOM    100  CB  LYS    24      -1.753   6.827  -2.456  1.00  0.00
ATOM    101  CG  LYS    24      -2.474   5.713  -1.716  1.00  0.00
ATOM    102  CD  LYS    24      -3.973   5.766  -1.963  1.00  0.00
ATOM    103  CE  LYS    24      -4.705   4.723  -1.135  1.00  0.00
ATOM    104  NZ  LYS    24      -6.179   4.778  -1.348  1.00  0.00
ATOM    105  O   LYS    24      -0.273   8.360  -4.180  1.00  0.00
ATOM    106  C   LYS    24       0.350   7.866  -3.241  1.00  0.00
ATOM    107  N   ASP    25       1.545   8.303  -2.855  1.00  0.00
ATOM    108  CA  ASP    25       2.187   9.410  -3.540  1.00  0.00
ATOM    109  CB  ASP    25       2.474  10.552  -2.561  1.00  0.00
ATOM    110  CG  ASP    25       1.208  11.184  -2.017  1.00  0.00
ATOM    111  OD1 ASP    25       0.559  10.561  -1.150  1.00  0.00
ATOM    112  OD2 ASP    25       0.865  12.300  -2.456  1.00  0.00
ATOM    113  O   ASP    25       4.029   9.740  -5.028  1.00  0.00
ATOM    114  C   ASP    25       3.508   9.020  -4.176  1.00  0.00
ATOM    115  N   GLU    26       4.056   7.877  -3.764  1.00  0.00
ATOM    116  CA  GLU    26       5.324   7.397  -4.301  1.00  0.00
ATOM    117  CB  GLU    26       5.279   7.359  -5.829  1.00  0.00
ATOM    118  CG  GLU    26       5.135   8.726  -6.480  1.00  0.00
ATOM    119  CD  GLU    26       5.018   8.644  -7.989  1.00  0.00
ATOM    120  OE1 GLU    26       5.019   7.516  -8.526  1.00  0.00
ATOM    121  OE2 GLU    26       4.926   9.708  -8.638  1.00  0.00
ATOM    122  O   GLU    26       6.292   9.222  -3.076  1.00  0.00
ATOM    123  C   GLU    26       6.474   8.306  -3.881  1.00  0.00
ATOM    124  N   LEU    27       7.656   8.047  -4.429  1.00  0.00
ATOM    125  CA  LEU    27       8.837   8.843  -4.114  1.00  0.00
ATOM    126  CB  LEU    27       9.953   7.953  -3.565  1.00  0.00
ATOM    127  CG  LEU    27       9.637   7.183  -2.282  1.00  0.00
ATOM    128  CD1 LEU    27      10.778   6.244  -1.922  1.00  0.00
ATOM    129  CD2 LEU    27       9.424   8.141  -1.119  1.00  0.00
ATOM    130  O   LEU    27       9.737   8.906  -6.338  1.00  0.00
ATOM    131  C   LEU    27       9.358   9.552  -5.361  1.00  0.00
ATOM    132  N   ILE    28       9.364  10.881  -5.329  1.00  0.00
ATOM    133  CA  ILE    28       9.819  11.669  -6.453  1.00  0.00
ATOM    134  CB  ILE    28       8.788  12.743  -6.844  1.00  0.00
ATOM    135  CG1 ILE    28       8.552  13.705  -5.678  1.00  0.00
ATOM    136  CG2 ILE    28       7.462  12.098  -7.216  1.00  0.00
ATOM    137  CD1 ILE    28       7.704  14.906  -6.039  1.00  0.00
ATOM    138  O   ILE    28      11.449  12.647  -4.988  1.00  0.00
ATOM    139  C   ILE    28      11.129  12.389  -6.145  1.00  0.00
ATOM    140  N   CYS    29      11.882  12.717  -7.195  1.00  0.00
ATOM    141  CA  CYS    29      13.154  13.413  -7.032  1.00  0.00
ATOM    142  CB  CYS    29      14.201  12.849  -7.994  1.00  0.00
ATOM    143  SG  CYS    29      14.619  11.114  -7.707  1.00  0.00
ATOM    144  O   CYS    29      12.324  15.286  -8.281  1.00  0.00
ATOM    145  C   CYS    29      12.990  14.907  -7.321  1.00  0.00
ATOM    146  N   LYS    30      13.588  15.776  -6.486  1.00  0.00
ATOM    147  CA  LYS    30      13.488  17.230  -6.662  1.00  0.00
ATOM    148  CB  LYS    30      13.921  17.956  -5.385  1.00  0.00
ATOM    149  CG  LYS    30      13.009  17.710  -4.193  1.00  0.00
ATOM    150  CD  LYS    30      13.496  18.457  -2.963  1.00  0.00
ATOM    151  CE  LYS    30      12.607  18.182  -1.762  1.00  0.00
ATOM    152  NZ  LYS    30      13.086  18.890  -0.543  1.00  0.00
ATOM    153  O   LYS    30      14.413  18.965  -8.041  1.00  0.00
ATOM    154  C   LYS    30      14.366  17.759  -7.796  1.00  0.00
ATOM    155  N   GLY    31      15.060  16.857  -8.488  1.00  0.00
ATOM    156  CA  GLY    31      15.930  17.249  -9.590  1.00  0.00
ATOM    157  O   GLY    31      14.812  17.410 -11.707  1.00  0.00
ATOM    158  C   GLY    31      15.419  16.687 -10.917  1.00  0.00
ATOM    159  N   ASP    32      15.658  15.397 -11.162  1.00  0.00
ATOM    160  CA  ASP    32      15.200  14.771 -12.401  1.00  0.00
ATOM    161  CB  ASP    32      15.774  13.359 -12.532  1.00  0.00
ATOM    162  CG  ASP    32      17.257  13.359 -12.845  1.00  0.00
ATOM    163  OD1 ASP    32      17.788  14.431 -13.205  1.00  0.00
ATOM    164  OD2 ASP    32      17.889  12.288 -12.728  1.00  0.00
ATOM    165  O   ASP    32      13.088  14.402 -13.478  1.00  0.00
ATOM    166  C   ASP    32      13.679  14.672 -12.431  1.00  0.00
ATOM    167  N   ARG    33      13.045  14.889 -11.281  1.00  0.00
ATOM    168  CA  ARG    33      11.600  14.813 -11.212  1.00  0.00
ATOM    169  CB  ARG    33      10.962  15.822 -12.170  1.00  0.00
ATOM    170  CG  ARG    33      11.350  17.266 -11.897  1.00  0.00
ATOM    171  CD  ARG    33      10.719  18.208 -12.910  1.00  0.00
ATOM    172  NE  ARG    33       9.281  18.352 -12.702  1.00  0.00
ATOM    173  CZ  ARG    33       8.733  19.186 -11.824  1.00  0.00
ATOM    174  NH1 ARG    33       7.414  19.250 -11.703  1.00  0.00
ATOM    175  NH2 ARG    33       9.505  19.956 -11.070  1.00  0.00
ATOM    176  O   ARG    33      10.233  13.307 -12.466  1.00  0.00
ATOM    177  C   ARG    33      11.082  13.440 -11.584  1.00  0.00
ATOM    178  N   LEU    34      11.594  12.414 -10.911  1.00  0.00
ATOM    179  CA  LEU    34      11.173  11.047 -11.183  1.00  0.00
ATOM    180  CB  LEU    34      12.364  10.090 -11.081  1.00  0.00
ATOM    181  CG  LEU    34      13.545  10.377 -12.010  1.00  0.00
ATOM    182  CD1 LEU    34      14.675   9.389 -11.764  1.00  0.00
ATOM    183  CD2 LEU    34      13.123  10.263 -13.468  1.00  0.00
ATOM    184  O   LEU    34       9.746  11.364  -9.285  1.00  0.00
ATOM    185  C   LEU    34      10.114  10.604 -10.180  1.00  0.00
ATOM    186  N   ALA    35       9.631   9.378 -10.340  1.00  0.00
ATOM    187  CA  ALA    35       8.611   8.833  -9.453  1.00  0.00
ATOM    188  CB  ALA    35       7.225   9.068 -10.030  1.00  0.00
ATOM    189  O   ALA    35       8.288   6.528 -10.039  1.00  0.00
ATOM    190  C   ALA    35       8.798   7.331  -9.260  1.00  0.00
ATOM    191  N   PHE    36       9.532   6.958  -8.215  1.00  0.00
ATOM    192  CA  PHE    36       9.783   5.552  -7.924  1.00  0.00
ATOM    193  CB  PHE    36      11.217   5.354  -7.428  1.00  0.00
ATOM    194  CG  PHE    36      12.262   5.618  -8.475  1.00  0.00
ATOM    195  CD1 PHE    36      12.837   6.871  -8.598  1.00  0.00
ATOM    196  CD2 PHE    36      12.668   4.614  -9.337  1.00  0.00
ATOM    197  CE1 PHE    36      13.798   7.114  -9.561  1.00  0.00
ATOM    198  CE2 PHE    36      13.629   4.857 -10.299  1.00  0.00
ATOM    199  CZ  PHE    36      14.193   6.101 -10.414  1.00  0.00
ATOM    200  O   PHE    36       8.675   5.654  -5.795  1.00  0.00
ATOM    201  C   PHE    36       8.834   5.034  -6.846  1.00  0.00
ATOM    202  N   PRO    37       8.207   3.894  -7.117  1.00  0.00
ATOM    203  CA  PRO    37       7.282   3.312  -6.161  1.00  0.00
ATOM    204  CB  PRO    37       7.758   3.848  -4.810  1.00  0.00
ATOM    205  CG  PRO    37       8.322   5.195  -5.122  1.00  0.00
ATOM    206  CD  PRO    37       8.994   5.066  -6.459  1.00  0.00
ATOM    207  O   PRO    37       5.230   4.412  -5.616  1.00  0.00
ATOM    208  C   PRO    37       5.846   3.716  -6.425  1.00  0.00
TER
END



