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     >>> no PHD predictions were used in model 2 
MODEL 2  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       0.448  -0.540   0.769  1.00  6.00 
ATOM      4  O   GLY     3      -0.432   0.080   1.366  1.00  6.00 
ATOM      5  N   ARG     4       1.666  -0.726   1.266  1.00  6.00 
ATOM      6  CA  ARG     4       2.077  -0.129   2.531  1.00  6.00 
ATOM      7  C   ARG     4       1.881   1.382   2.517  1.00  6.00 
ATOM      8  O   ARG     4       1.470   1.974   3.515  1.00  6.00 
ATOM      9  N   GLU     5       2.180   2.001   1.380  1.00  5.60 
ATOM     10  CA  GLU     5       1.991   3.438   1.217  1.00  5.60 
ATOM     11  C   GLU     5       0.514   3.807   1.256  1.00  5.60 
ATOM     12  O   GLU     5       0.073   4.550   2.132  1.00  5.60 
ATOM     13  N   GLY     6      -0.246   3.284   0.299  1.00  4.25 
ATOM     14  CA  GLY     6      -1.673   3.574   0.210  1.00  4.25 
ATOM     15  C   GLY     6      -2.402   3.144   1.477  1.00  4.25 
ATOM     16  O   GLY     6      -3.312   3.830   1.943  1.00  4.25 
ATOM     17  N   VAL     7      -1.999   2.005   2.028  1.00  4.20 
ATOM     18  CA  VAL     7      -2.604   1.489   3.250  1.00  4.20 
ATOM     19  C   VAL     7      -2.592   2.537   4.356  1.00  4.20 
ATOM     20  O   VAL     7      -3.633   2.862   4.927  1.00  4.20 
ATOM     21  CB  VAL     7      -1.886   0.228   3.705  1.00  4.20 
ATOM     22  N   LEU     8      -1.409   3.062   4.654  1.00  4.20 
ATOM     23  CA  LEU     8      -1.257   4.060   5.707  1.00  4.20 
ATOM     24  C   LEU     8      -2.231   5.215   5.516  1.00  4.20 
ATOM     25  O   LEU     8      -2.857   5.675   6.471  1.00  4.20 
ATOM     26  N   LYS     9      -2.354   5.680   4.278  1.00  3.95 
ATOM     27  CA  LYS     9      -3.286   6.753   3.952  1.00  3.95 
ATOM     28  C   LYS     9      -4.730   6.279   4.053  1.00  3.95 
ATOM     29  O   LYS     9      -5.598   7.001   4.543  1.00  3.95 
ATOM     30  CB  LYS     9      -3.001   7.298   2.561  1.00  3.95 
ATOM     31  N   LYS    10      -4.982   5.060   3.587  1.00  3.70 
ATOM     32  CA  LYS    10      -6.323   4.489   3.618  1.00  3.70 
ATOM     33  C   LYS    10      -6.735   4.130   5.040  1.00  3.70 
ATOM     34  O   LYS    10      -7.859   4.405   5.459  1.00  3.70 
ATOM     35  CB  LYS    10      -6.400   3.268   2.716  1.00  3.70 
ATOM     36  N   LEU    11      -5.819   3.510   5.777  1.00  3.70 
ATOM     37  CA  LEU    11      -6.096   3.085   7.144  1.00  3.70 
ATOM     38  C   LEU    11      -6.100   4.271   8.100  1.00  3.70 
ATOM     39  O   LEU    11      -6.614   4.180   9.215  1.00  3.70 
ATOM     40  CB  LEU    11      -5.081   2.044   7.591  1.00  3.70 
ATOM     41  N   ARG    12      -5.522   5.383   7.658  1.00  2.75 
ATOM     42  CA  ARG    12      -5.420   6.576   8.489  1.00  2.75 
ATOM     43  C   ARG    12      -6.263   7.713   7.926  1.00  2.75 
ATOM     44  O   ARG    12      -7.157   7.491   7.109  1.00  2.75 
ATOM     45  CB  ARG    12      -3.968   7.006   8.624  1.00  2.75 
ATOM     46  N   ALA    13      -5.974   8.932   8.368  1.00  1.80 
ATOM     47  CA  ALA    13      -6.824  10.078   8.067  1.00  1.80 
ATOM     48  C   ALA    13      -6.220  10.937   6.963  1.00  1.80 
ATOM     49  O   ALA    13      -6.805  11.939   6.553  1.00  1.80 
ATOM     50  CB  ALA    13      -7.059  10.908   9.319  1.00  1.80 
ATOM     51  N   VAL    14      -5.044  10.540   6.488  1.00  2.65 
ATOM     52  CA  VAL    14      -4.333  11.302   5.469  1.00  2.65 
ATOM     53  C   VAL    14      -5.209  11.538   4.245  1.00  2.65 
ATOM     54  O   VAL    14      -5.274  12.650   3.721  1.00  2.65 
ATOM     55  CB  VAL    14      -3.048  10.591   5.076  1.00  2.65 
ATOM     56  N   GLU    15      -5.879  10.483   3.792  1.00  3.50 
ATOM     57  CA  GLU    15      -6.768  10.578   2.640  1.00  3.50 
ATOM     58  C   GLU    15      -7.838  11.640   2.857  1.00  3.50 
ATOM     59  O   GLU    15      -8.081  12.476   1.986  1.00  3.50 
ATOM     60  CB  GLU    15      -7.408   9.229   2.352  1.00  3.50 
ATOM     61  N   ASN    16      -8.476  11.602   4.021  1.00  3.50 
ATOM     62  CA  ASN    16      -9.485  12.593   4.376  1.00  3.50 
ATOM     63  C   ASN    16      -8.858  13.966   4.584  1.00  3.50 
ATOM     64  O   ASN    16      -9.402  14.980   4.145  1.00  3.50 
ATOM     65  CB  ASN    16     -10.241  12.158   5.621  1.00  3.50 
ATOM     66  N   GLU    17      -7.713  13.992   5.258  1.00  3.60 
ATOM     67  CA  GLU    17      -7.008  15.240   5.522  1.00  3.60 
ATOM     68  C   GLU    17      -6.580  15.916   4.226  1.00  3.60 
ATOM     69  O   GLU    17      -6.449  17.139   4.166  1.00  3.60 
ATOM     70  CB  GLU    17      -5.803  14.990   6.415  1.00  3.60 
ATOM     71  N   LEU    18      -6.362  15.113   3.190  1.00  3.70 
ATOM     72  CA  LEU    18      -5.963  15.634   1.888  1.00  3.70 
ATOM     73  C   LEU    18      -7.104  16.397   1.226  1.00  3.70 
ATOM     74  O   LEU    18      -6.931  17.534   0.789  1.00  3.70 
ATOM     75  CB  LEU    18      -5.486  14.504   0.989  1.00  3.70 
ATOM     76  N   HIS    19      -8.269  15.763   1.154  1.00  4.25 
ATOM     77  CA  HIS    19      -9.462  16.410   0.620  1.00  4.25 
ATOM     78  C   HIS    19      -9.871  17.602   1.475  1.00  4.25 
ATOM     79  O   HIS    19     -10.236  18.656   0.954  1.00  4.25 
ATOM     80  CB  HIS    19     -10.605  15.412   0.516  1.00  4.25 
ATOM     81  N   TYR    20      -9.810  17.429   2.791  1.00  4.10 
ATOM     82  CA  TYR    20     -10.196  18.483   3.721  1.00  4.10 
ATOM     83  C   TYR    20      -9.068  19.488   3.916  1.00  4.10 
ATOM     84  O   TYR    20      -9.253  20.531   4.543  1.00  4.10 
ATOM     85  CB  TYR    20     -10.613  17.885   5.056  1.00  4.10 
ATOM     86  N   ASN    21      -7.897  19.166   3.376  1.00  3.40 
ATOM     87  CA  ASN    21      -6.692  19.942   3.642  1.00  3.40 
ATOM     88  C   ASN    21      -6.830  21.369   3.126  1.00  3.40 
ATOM     89  O   ASN    21      -6.348  22.314   3.750  1.00  3.40 
ATOM     90  CB  ASN    21      -5.479  19.267   3.022  1.00  3.40 
ATOM     91  N   LYS    22      -7.490  21.518   1.982  1.00  2.95 
ATOM     92  CA  LYS    22      -7.637  22.821   1.347  1.00  2.95 
ATOM     93  C   LYS    22      -8.648  23.685   2.089  1.00  2.95 
ATOM     94  O   LYS    22      -8.372  24.840   2.415  1.00  2.95 
ATOM     95  CB  LYS    22      -8.043  22.658  -0.110  1.00  2.95 
ATOM     96  N   SER    23      -9.822  23.120   2.352  1.00  2.50 
ATOM     97  CA  SER    23     -10.868  23.829   3.079  1.00  2.50 
ATOM     98  C   SER    23     -10.395  24.233   4.469  1.00  2.50 
ATOM     99  O   SER    23     -10.728  25.312   4.959  1.00  2.50 
ATOM    100  CB  SER    23     -12.122  22.973   3.171  1.00  2.50 
ATOM    101  N   LEU    24      -9.617  23.360   5.102  1.00  2.50 
ATOM    102  CA  LEU    24      -9.073  23.638   6.426  1.00  2.50 
ATOM    103  C   LEU    24      -7.746  24.379   6.332  1.00  2.50 
ATOM    104  O   LEU    24      -7.206  24.834   7.340  1.00  2.50 
ATOM    105  CB  LEU    24      -8.907  22.346   7.211  1.00  2.50 
ATOM    106  N   LEU    25      -7.225  24.497   5.115  1.00  2.50 
ATOM    107  CA  LEU    25      -5.942  25.152   4.892  1.00  2.50 
ATOM    108  C   LEU    25      -5.882  26.503   5.594  1.00  2.50 
ATOM    109  O   LEU    25      -4.881  26.842   6.225  1.00  2.50 
ATOM    110  CB  LEU    25      -5.682  25.315   3.402  1.00  2.50 
ATOM    111  N   GLU    26      -6.960  27.271   5.480  1.00  2.30 
ATOM    112  CA  GLU    26      -7.040  28.580   6.118  1.00  2.30 
ATOM    113  C   GLU    26      -6.973  28.457   7.635  1.00  2.30 
ATOM    114  O   GLU    26      -6.044  28.959   8.267  1.00  2.30 
ATOM    115  CB  GLU    26      -8.312  29.299   5.697  1.00  2.30 
ATOM    116  N   GLU    27      -7.965  27.789   8.214  1.00  2.10 
ATOM    117  CA  GLU    27      -8.025  27.607   9.659  1.00  2.10 
ATOM    118  C   GLU    27      -6.888  26.720  10.150  1.00  2.10 
ATOM    119  O   GLU    27      -6.282  26.988  11.188  1.00  2.10 
ATOM    120  CB  GLU    27      -9.369  27.023  10.064  1.00  2.10 
ATOM    121  N   VAL    28      -6.604  25.661   9.400  1.00  1.85 
ATOM    122  CA  VAL    28      -5.544  24.727   9.762  1.00  1.85 
ATOM    123  C   VAL    28      -4.180  25.403   9.726  1.00  1.85 
ATOM    124  O   VAL    28      -3.254  24.991  10.424  1.00  1.85 
ATOM    125  CB  VAL    28      -5.565  23.519   8.839  1.00  1.85 
ATOM    126  N   LYS    29      -4.061  26.442   8.906  1.00  1.60 
ATOM    127  CA  LYS    29      -2.822  27.204   8.810  1.00  1.60 
ATOM    128  C   LYS    29      -2.553  27.983  10.091  1.00  1.60 
ATOM    129  O   LYS    29      -1.402  28.172  10.484  1.00  1.60 
ATOM    130  CB  LYS    29      -2.869  28.145   7.615  1.00  1.60 
ATOM    131  N   ASP    30      -3.622  28.434  10.739  1.00  1.60 
ATOM    132  CA  ASP    30      -3.503  29.188  11.981  1.00  1.60 
ATOM    133  C   ASP    30      -2.951  28.318  13.103  1.00  1.60 
ATOM    134  O   ASP    30      -2.075  28.743  13.856  1.00  1.60 
ATOM    135  CB  ASP    30      -4.850  29.774  12.376  1.00  1.60 
ATOM    136  N   GLU    31      -3.470  27.100  13.210  1.00  1.60 
ATOM    137  CA  GLU    31      -3.017  26.162  14.231  1.00  1.60 
ATOM    138  C   GLU    31      -1.690  25.523  13.842  1.00  1.60 
ATOM    139  O   GLU    31      -0.796  25.372  14.675  1.00  1.60 
ATOM    140  CB  GLU    31      -4.072  25.093  14.473  1.00  1.60 
ATOM    141  N   LEU    32      -1.569  25.147  12.574  1.00  1.60 
ATOM    142  CA  LEU    32      -0.343  24.542  12.067  1.00  1.60 
ATOM    143  C   LEU    32       0.841  25.488  12.219  1.00  1.60 
ATOM    144  O   LEU    32       1.902  25.098  12.708  1.00  1.60 
ATOM    145  CB  LEU    32      -0.515  24.133  10.613  1.00  1.60 
ATOM    146  N   GLN    33       0.655  26.733  11.795  1.00  1.85 
ATOM    147  CA  GLN    33       1.691  27.751  11.929  1.00  1.85 
ATOM    148  C   GLN    33       2.073  27.960  13.388  1.00  1.85 
ATOM    149  O   GLN    33       3.244  28.158  13.711  1.00  1.85 
ATOM    150  CB  GLN    33       1.231  29.060  11.306  1.00  1.85 
ATOM    151  N   LYS    34       1.077  27.916  14.267  1.00  2.10 
ATOM    152  CA  LYS    34       1.320  27.977  15.704  1.00  2.10 
ATOM    153  C   LYS    34       2.104  26.761  16.181  1.00  2.10 
ATOM    154  O   LYS    34       3.120  26.895  16.864  1.00  2.10 
ATOM    155  CB  LYS    34       0.005  28.093  16.459  1.00  2.10 
ATOM    156  N   MET    35       1.626  25.576  15.820  1.00  2.10 
ATOM    157  CA  MET    35       2.309  24.335  16.169  1.00  2.10 
ATOM    158  C   MET    35       3.686  24.264  15.523  1.00  2.10 
ATOM    159  O   MET    35       4.620  23.697  16.090  1.00  2.10 
ATOM    160  CB  MET    35       1.467  23.135  15.765  1.00  2.10 
ATOM    161  N   ARG    36       3.806  24.839  14.331  1.00  2.95 
ATOM    162  CA  ARG    36       5.066  24.830  13.599  1.00  2.95 
ATOM    163  C   ARG    36       6.149  25.587  14.357  1.00  2.95 
ATOM    164  O   ARG    36       7.204  25.033  14.669  1.00  2.95 
ATOM    165  CB  ARG    36       4.877  25.421  12.210  1.00  2.95 
ATOM    166  N   GLN    37       5.884  26.855  14.650  1.00  6.00 
ATOM    167  CA  GLN    37       6.802  27.668  15.438  1.00  6.00 
ATOM    168  C   GLN    37       6.051  28.526  16.448  1.00  6.00 
ATOM    169  O   GLN    37       4.882  28.856  16.249  1.00  6.00 
ATOM    170  CB  GLN    37       7.653  28.540  14.527  1.00  6.00 
TER 
END 
