PFRMAT TS 
TARGET T0084 
AUTHOR 9271-4485-8460 
REMARK 
METHOD  Automated I-SITES + ROSETTA 
METHOD  ========================================================= 
METHOD  Predictions from this group are of local and 
METHOD  supersecondary structure. They should be evaluated 
METHOD  on an approximate length scale of 20-30 residues. Although 
METHOD  Some effort has been made to pack the local structure 
METHOD  predictions into a globular form, the effectiveness 
METHOD  of this procedure is untested. 
METHOD  ========================================================= 
METHOD Steps used to generate TS predictions 
METHOD (1) Psi-blast was used to obtain an alignment 
METHOD (2) The PHD prediction server was used to obtain a 3-state  
METHOD     prediction (optional) 
METHOD (3) The I-sites method (JMB 281(3):565-577) 
METHOD     was used to predict backbone angles and  
METHOD     confidences. Backbone angle confidnces are reflected in 
METHOD     the B-column of the PDB output. B = 1.00 + (1.00 - confidence)*10 
METHOD     except unpredicted residus (B = 0.00) 
METHOD (4) Non-conserved non-polar sidechains were converted to their 
METHOD     most likely polar counterpart. This would, we hope, restrict 
METHOD     core residues to conserved non-polar sidechains. 
METHOD (5) Fragment insertion Monte Carlo folding (ROSETTA, Simons et al 
METHOD     PNAS, in press) was used to build a 3D structure from the 
METHOD     fragment library output by I-sites. Residues with I-sites 
METHOD     confidences > 0.50 were restrained to their predicted backbone 
METHOD     angles. For longer sequences, the protein was broken up into 
METHOD     segments containing 50 un-restrained residues (typically 100 
METHOD     residues).  
METHOD (6) The 3D structure with the best score was selected, its 
METHOD     sequence replaced with the original one. For long sequences 
METHOD     A simple genetic algorithm was employed to find the 
METHOD     optimum points of recombination, using the same scoring function 
METHOD     as above (ROSETTA). 
METHOD  
METHOD >>>>THIS METHOD IS TOTALLY AUTOMATED!! <<<< 
METHOD In constrast to earlier CASP3 
METHOD methods from this (D. Baker) lab. The submissions from this 
METHOD group ("C.Bystroff") are made automatically with no manual 
METHOD intervention. The method will be available via WWW server, 
METHOD after CASP3. The URL is http://ganesh.bchem.washington.edu/ 
METHOD ~bystroff/Isites/ISLserver2.html 
METHOD     >>> PHD predictions were used (model 1) 
MODEL 1  REFINED 
PARENT N/A 
ATOM      1  N   GLY     3       1.221  -0.771  -1.555  1.00  6.00 
ATOM      2  CA  GLY     3       0.181  -1.145  -0.603  1.00  6.00 
ATOM      3  C   GLY     3      -1.171  -0.578  -1.014  1.00  6.00 
ATOM      4  O   GLY     3      -2.078  -0.451  -0.191  1.00  6.00 
ATOM      5  N   ARG     4      -1.301  -0.237  -2.291  1.00  6.00 
ATOM      6  CA  ARG     4      -2.557   0.276  -2.824  1.00  6.00 
ATOM      7  C   ARG     4      -3.732  -0.598  -2.404  1.00  6.00 
ATOM      8  O   ARG     4      -4.733  -0.104  -1.885  1.00  6.00 
ATOM      9  CB  ARG     4      -2.487   0.383  -4.339  1.00  6.00 
ATOM     10  N   GLU     5      -3.604  -1.901  -2.633  1.00  5.60 
ATOM     11  CA  GLU     5      -4.648  -2.850  -2.263  1.00  5.60 
ATOM     12  C   GLU     5      -4.792  -2.948  -0.750  1.00  5.60 
ATOM     13  O   GLU     5      -5.890  -3.159  -0.234  1.00  5.60 
ATOM     14  CB  GLU     5      -4.356  -4.218  -2.861  1.00  5.60 
ATOM     15  N   GLY     6      -3.677  -2.796  -0.043  1.00  4.25 
ATOM     16  CA  GLY     6      -3.680  -2.854   1.413  1.00  4.25 
ATOM     17  C   GLY     6      -4.380  -1.642   2.012  1.00  4.25 
ATOM     18  O   GLY     6      -5.127  -1.761   2.984  1.00  4.25 
ATOM     19  N   VAL     7      -4.133  -0.474   1.429  1.00  4.20 
ATOM     20  CA  VAL     7      -4.728   0.766   1.914  1.00  4.20 
ATOM     21  C   VAL     7      -6.249   0.698   1.877  1.00  4.20 
ATOM     22  O   VAL     7      -6.920   1.069   2.840  1.00  4.20 
ATOM     23  CB  VAL     7      -4.228   1.948   1.098  1.00  4.20 
ATOM     24  N   LEU     8      -6.789   0.223   0.759  1.00  4.20 
ATOM     25  CA  LEU     8      -8.233   0.126   0.587  1.00  4.20 
ATOM     26  C   LEU     8      -8.873  -0.651   1.730  1.00  4.20 
ATOM     27  O   LEU     8      -9.804  -0.169   2.376  1.00  4.20 
ATOM     28  CB  LEU     8      -8.565  -0.522  -0.748  1.00  4.20 
ATOM     29  N   LYS     9      -8.370  -1.856   1.975  1.00  3.95 
ATOM     30  CA  LYS     9      -8.895  -2.704   3.039  1.00  3.95 
ATOM     31  C   LYS     9      -8.412  -2.235   4.405  1.00  3.95 
ATOM     32  O   LYS     9      -9.160  -2.266   5.383  1.00  3.95 
ATOM     33  CB  LYS     9      -8.502  -4.154   2.804  1.00  3.95 
ATOM     34  N   LYS    10      -7.157  -1.803   4.468  1.00  3.70 
ATOM     35  CA  LYS    10      -6.558  -1.368   5.723  1.00  3.70 
ATOM     36  C   LYS    10      -6.861   0.100   5.998  1.00  3.70 
ATOM     37  O   LYS    10      -6.521   0.626   7.058  1.00  3.70 
ATOM     38  CB  LYS    10      -5.056  -1.607   5.706  1.00  3.70 
ATOM     39  N   LEU    11      -7.500   0.757   5.037  1.00  3.70 
ATOM     40  CA  LEU    11      -7.817   2.175   5.158  1.00  3.70 
ATOM     41  C   LEU    11      -8.552   2.465   6.460  1.00  3.70 
ATOM     42  O   LEU    11      -8.534   3.592   6.957  1.00  3.70 
ATOM     43  CB  LEU    11      -8.641   2.638   3.967  1.00  3.70 
ATOM     44  N   ARG    12      -9.201   1.443   7.009  1.00  2.75 
ATOM     45  CA  ARG    12      -9.929   1.583   8.264  1.00  2.75 
ATOM     46  C   ARG    12      -8.974   1.705   9.444  1.00  2.75 
ATOM     47  O   ARG    12      -9.092   2.621  10.258  1.00  2.75 
ATOM     48  CB  ARG    12     -10.874   0.408   8.462  1.00  2.75 
ATOM     49  N   ALA    13      -8.029   0.774   9.533  1.00  1.80 
ATOM     50  CA  ALA    13      -7.062   0.766  10.624  1.00  1.80 
ATOM     51  C   ALA    13      -5.652   1.030  10.112  1.00  1.80 
ATOM     52  O   ALA    13      -4.671   0.795  10.817  1.00  1.80 
ATOM     53  CB  ALA    13      -7.118  -0.556  11.372  1.00  1.80 
ATOM     54  N   VAL    14      -5.557   1.519   8.880  1.00  2.65 
ATOM     55  CA  VAL    14      -4.265   1.765   8.251  1.00  2.65 
ATOM     56  C   VAL    14      -3.366   2.605   9.149  1.00  2.65 
ATOM     57  O   VAL    14      -2.243   2.211   9.463  1.00  2.65 
ATOM     58  CB  VAL    14      -4.453   2.442   6.902  1.00  2.65 
ATOM     59  N   GLU    15      -3.866   3.766   9.559  1.00  3.50 
ATOM     60  CA  GLU    15      -3.102   4.672  10.408  1.00  3.50 
ATOM     61  C   GLU    15      -2.633   3.974  11.677  1.00  3.50 
ATOM     62  O   GLU    15      -1.483   4.125  12.092  1.00  3.50 
ATOM     63  CB  GLU    15      -3.930   5.901  10.751  1.00  3.50 
ATOM     64  N   ASN    16      -3.529   3.209  12.292  1.00  3.50 
ATOM     65  CA  ASN    16      -3.209   2.488  13.518  1.00  3.50 
ATOM     66  C   ASN    16      -2.378   1.245  13.224  1.00  3.50 
ATOM     67  O   ASN    16      -1.516   0.862  14.015  1.00  3.50 
ATOM     68  CB  ASN    16      -4.482   2.114  14.261  1.00  3.50 
ATOM     69  N   GLU    17      -2.645   0.617  12.084  1.00  3.60 
ATOM     70  CA  GLU    17      -1.895  -0.561  11.664  1.00  3.60 
ATOM     71  C   GLU    17      -0.394  -0.309  11.726  1.00  3.60 
ATOM     72  O   GLU    17       0.330  -0.987  12.456  1.00  3.60 
ATOM     73  CB  GLU    17      -2.307  -0.980  10.262  1.00  3.60 
ATOM     74  N   LEU    18       0.069   0.669  10.955  1.00  3.70 
ATOM     75  CA  LEU    18       1.483   1.024  10.935  1.00  3.70 
ATOM     76  C   LEU    18       1.959   1.471  12.311  1.00  3.70 
ATOM     77  O   LEU    18       3.074   1.153  12.726  1.00  3.70 
ATOM     78  CB  LEU    18       1.742   2.112   9.903  1.00  3.70 
ATOM     79  N   HIS    19       1.109   2.211  13.014  1.00  4.25 
ATOM     80  CA  HIS    19       1.413   2.645  14.373  1.00  4.25 
ATOM     81  C   HIS    19       1.550   1.454  15.313  1.00  4.25 
ATOM     82  O   HIS    19       2.400   1.448  16.203  1.00  4.25 
ATOM     83  CB  HIS    19       0.343   3.601  14.876  1.00  4.25 
ATOM     84  N   TYR    20       0.706   0.448  15.112  1.00  4.10 
ATOM     85  CA  TYR    20       0.804  -0.797  15.865  1.00  4.10 
ATOM     86  C   TYR    20       2.085  -1.547  15.526  1.00  4.10 
ATOM     87  O   TYR    20       2.696  -2.174  16.391  1.00  4.10 
ATOM     88  CB  TYR    20      -0.412  -1.672  15.603  1.00  4.10 
ATOM     89  N   ASN    21       2.487  -1.480  14.261  1.00  3.40 
ATOM     90  CA  ASN    21       3.672  -2.190  13.795  1.00  3.40 
ATOM     91  C   ASN    21       4.865  -1.926  14.705  1.00  3.40 
ATOM     92  O   ASN    21       5.531  -2.858  15.157  1.00  3.40 
ATOM     93  CB  ASN    21       3.997  -1.795  12.363  1.00  3.40 
ATOM     94  N   LYS    22       5.131  -0.652  14.970  1.00  2.95 
ATOM     95  CA  LYS    22       6.178  -0.266  15.909  1.00  2.95 
ATOM     96  C   LYS    22       5.886  -0.796  17.307  1.00  2.95 
ATOM     97  O   LYS    22       6.743  -1.415  17.937  1.00  2.95 
ATOM     98  CB  LYS    22       6.336   1.246  15.934  1.00  2.95 
ATOM     99  N   SER    23       4.672  -0.547  17.787  1.00  2.50 
ATOM    100  CA  SER    23       4.268  -0.993  19.115  1.00  2.50 
ATOM    101  C   SER    23       4.135  -2.509  19.170  1.00  2.50 
ATOM    102  O   SER    23       4.752  -3.166  20.009  1.00  2.50 
ATOM    103  CB  SER    23       2.961  -0.329  19.522  1.00  2.50 
ATOM    104  N   LEU    24       3.325  -3.060  18.273  1.00  2.50 
ATOM    105  CA  LEU    24       3.077  -4.497  18.244  1.00  2.50 
ATOM    106  C   LEU    24       4.383  -5.280  18.196  1.00  2.50 
ATOM    107  O   LEU    24       4.617  -6.166  19.019  1.00  2.50 
ATOM    108  CB  LEU    24       2.195  -4.859  17.060  1.00  2.50 
ATOM    109  N   LEU    25       5.230  -4.950  17.227  1.00  2.50 
ATOM    110  CA  LEU    25       6.509  -5.629  17.063  1.00  2.50 
ATOM    111  C   LEU    25       7.422  -5.381  18.257  1.00  2.50 
ATOM    112  O   LEU    25       8.121  -6.285  18.715  1.00  2.50 
ATOM    113  CB  LEU    25       7.185  -5.185  15.775  1.00  2.50 
ATOM    114  N   GLU    26       7.412  -4.150  18.757  1.00  2.30 
ATOM    115  CA  GLU    26       8.242  -3.779  19.897  1.00  2.30 
ATOM    116  C   GLU    26       7.843  -4.556  21.145  1.00  2.30 
ATOM    117  O   GLU    26       8.675  -5.211  21.774  1.00  2.30 
ATOM    118  CB  GLU    26       8.155  -2.282  20.152  1.00  2.30 
ATOM    119  N   GLU    27       6.565  -4.479  21.501  1.00  2.10 
ATOM    120  CA  GLU    27       6.054  -5.168  22.680  1.00  2.10 
ATOM    121  C   GLU    27       6.003  -6.674  22.458  1.00  2.10 
ATOM    122  O   GLU    27       6.133  -7.455  23.401  1.00  2.10 
ATOM    123  CB  GLU    27       4.678  -4.637  23.050  1.00  2.10 
ATOM    124  N   VAL    28       5.811  -7.077  21.206  1.00  1.85 
ATOM    125  CA  VAL    28       5.796  -8.491  20.850  1.00  1.85 
ATOM    126  C   VAL    28       7.167  -9.124  21.047  1.00  1.85 
ATOM    127  O   VAL    28       7.329 -10.039  21.855  1.00  1.85 
ATOM    128  CB  VAL    28       5.327  -8.671  19.415  1.00  1.85 
ATOM    129  N   LYS    29       8.152  -8.632  20.303  1.00  1.60 
ATOM    130  CA  LYS    29       9.520  -9.126  20.419  1.00  1.60 
ATOM    131  C   LYS    29       9.952  -9.212  21.877  1.00  1.60 
ATOM    132  O   LYS    29      10.499 -10.225  22.313  1.00  1.60 
ATOM    133  CB  LYS    29      10.472  -8.238  19.633  1.00  1.60 
ATOM    134  N   ASP    30       9.705  -8.144  22.627  1.00  1.60 
ATOM    135  CA  ASP    30      10.047  -8.106  24.044  1.00  1.60 
ATOM    136  C   ASP    30       9.142  -9.025  24.854  1.00  1.60 
ATOM    137  O   ASP    30       9.602  -9.732  25.751  1.00  1.60 
ATOM    138  CB  ASP    30       9.969  -6.682  24.570  1.00  1.60 
ATOM    139  N   GLU    31       7.853  -9.009  24.534  1.00  1.60 
ATOM    140  CA  GLU    31       6.875  -9.820  25.250  1.00  1.60 
ATOM    141  C   GLU    31       7.324 -11.273  25.338  1.00  1.60 
ATOM    142  O   GLU    31       7.150 -11.925  26.368  1.00  1.60 
ATOM    143  CB  GLU    31       5.513  -9.723  24.581  1.00  1.60 
ATOM    144  N   LEU    32       7.900 -11.777  24.252  1.00  1.60 
ATOM    145  CA  LEU    32       8.356 -13.160  24.198  1.00  1.60 
ATOM    146  C   LEU    32       9.436 -13.425  25.239  1.00  1.60 
ATOM    147  O   LEU    32       9.413 -14.447  25.925  1.00  1.60 
ATOM    148  CB  LEU    32       8.866 -13.496  22.805  1.00  1.60 
ATOM    149  N   GLN    33      10.382 -12.499  25.351  1.00  1.85 
ATOM    150  CA  GLN    33      11.508 -12.661  26.263  1.00  1.85 
ATOM    151  C   GLN    33      11.032 -12.950  27.681  1.00  1.85 
ATOM    152  O   GLN    33      11.479 -13.906  28.314  1.00  1.85 
ATOM    153  CB  GLN    33      12.392 -11.423  26.240  1.00  1.85 
ATOM    154  N   LYS    34      10.123 -12.115  28.176  1.00  2.10 
ATOM    155  CA  LYS    34       9.569 -12.292  29.513  1.00  2.10 
ATOM    156  C   LYS    34       8.557 -13.430  29.544  1.00  2.10 
ATOM    157  O   LYS    34       8.615 -14.301  30.411  1.00  2.10 
ATOM    158  CB  LYS    34       8.932 -10.999  29.997  1.00  2.10 
ATOM    159  N   MET    35       7.629 -13.415  28.593  1.00  2.10 
ATOM    160  CA  MET    35       6.592 -14.438  28.519  1.00  2.10 
ATOM    161  C   MET    35       7.196 -15.820  28.309  1.00  2.10 
ATOM    162  O   MET    35       6.661 -16.821  28.786  1.00  2.10 
ATOM    163  CB  MET    35       5.605 -14.113  27.409  1.00  2.10 
ATOM    164  N   ARG    36       8.313 -15.870  27.591  1.00  2.95 
ATOM    165  CA  ARG    36       9.070 -17.106  27.436  1.00  2.95 
ATOM    166  C   ARG    36       9.364 -17.745  28.787  1.00  2.95 
ATOM    167  O   ARG    36       9.000 -18.895  29.033  1.00  2.95 
ATOM    168  CB  ARG    36      10.362 -16.845  26.677  1.00  2.95 
ATOM    169  N   GLN    37      10.028 -16.994  29.659  1.00  6.00 
ATOM    170  CA  GLN    37      10.393 -17.494  30.979  1.00  6.00 
ATOM    171  C   GLN    37      10.421 -16.370  32.006  1.00  6.00 
ATOM    172  O   GLN    37      10.918 -15.277  31.732  1.00  6.00 
ATOM    173  CB  GLN    37      11.740 -18.199  30.924  1.00  6.00 
TER 
END 
