PFRMAT TS 
TARGET T0065 
AUTHOR 3363-3494-1306 
METHOD During the last year, we developed a new approach to reduced  
METHOD representation and Monte Carlo simulation of protein structures.   
METHOD It builds on the very well known fact that intra-protein  
METHOD interactions are rather specific for amino acid side chains and  
METHOD rather generic for the main chain units.  Thus, the proposed lattice  
METHOD model of polypeptides assumes explicit representation only for  
METHOD the side chains, where particular side groups are represented  
METHOD as clusters of occupied points on the underlying simple cubic  
METHOD lattice (1,2).  A new, knowledge-based force field has been  
METHOD developed for this model based on local distance geometry,  
METHOD statistics of side chain contacts in known protein structures  
METHOD and some multibody correlations observed in real proteins.   
METHOD The model is a purely lattice type and in spite of the same  
METHOD level of resolution as more complex reduced models, allows for  
METHOD about hundred times faster Monte Carlo sampling, thereby enabling  
METHOD the study of much larger protein systems. 
METHOD The important part of this methodology is the development of  
METHOD potentials that are characteristic for a given protein sequence.  
METHOD First, from the structural database, the collection of sequence  
METHOD fragments that are most similar to particular (overlapping)  
METHOD sequence fragments of the query protein are selected.  These  
METHOD fragments, presumably also similar structurally, are then used to  
METHOD build statistical potentials describing secondary propensities  
METHOD of the query sequence.  In a somewhat similar fashion, the  
METHOD long-range potentials could be derived.  
METHOD The model force filed is supplemented with theoretically predicted  
METHOD tertiary restraints derived from multiple sequence alignments  
METHOD and a combination of correlated mutation analysis and fragment  
METHOD threading procedures (3).  A number of folds (20-40) were generated  
METHOD and the  lowest energy structure from the best defined clusters  
METHOD were selected for all atom reconstruction. 
METHOD (1) A.Kolinski and J. Skolnick,  
METHOD Assembly of protein structure from sparse experimental data:  
METHOD An efficient Monte Carlo model, Proteins, 32, 475-494 (1998). 
METHOD (2) A.Kolinski, L. Jaroszewski, P. Rotkiewicz, J. Skolnick,  
METHOD An efficient Monte Carlo model of protein chains. Modeling  
METHOD the short-range correlations between side group centers  
METHOD of mass, J. Chem. Phys., in press (1998). 
METHOD (3) A.Ortiz, A. Kolinski, J. Skolnick,  
METHOD Fold assembly of small proteins using Monte Carlo simulations  
METHOD driven by restraints derived from multiple sequence alignments,  
METHOD J. Mol. Biol., 277:419-448 (1998). 
MODEL  2 
PARENT N/A 
ATOM      1  N   MET B   1       3.906 -13.199  -3.132  1.00  5.00 
ATOM      2  CA  MET B   1       2.855 -12.198  -3.032  1.00  5.00 
ATOM      7  C   MET B   1       3.239 -11.130  -2.086  1.00  5.00 
ATOM      8  O   MET B   1       3.180  -9.951  -2.403  1.00  5.00 
ATOM      9  N   LYS B   2       3.739 -11.524  -0.919  1.00  5.00 
ATOM     10  CA  LYS B   2       4.124 -10.591   0.065  1.00  5.00 
ATOM     16  C   LYS B   2       5.543 -10.443  -0.170  1.00  5.00 
ATOM     17  O   LYS B   2       6.231  -9.978   0.716  1.00  5.00 
ATOM     18  N   ASN B   3       5.987 -10.945  -1.328  1.00  5.00 
ATOM     19  CA  ASN B   3       7.297 -10.935  -1.844  1.00  5.00 
ATOM     24  C   ASN B   3       6.916 -11.206  -3.234  1.00  5.00 
ATOM     25  O   ASN B   3       7.719 -11.662  -4.035  1.00  5.00 
ATOM     26  N   ALA B   4       5.632 -10.892  -3.510  1.00  5.00 
ATOM     27  CA  ALA B   4       5.002 -11.077  -4.780  1.00  5.00 
ATOM     29  C   ALA B   4       5.831 -10.257  -5.421  1.00  5.00 
ATOM     30  O   ALA B   4       6.741 -10.678  -6.112  1.00  5.00 
ATOM     31  N   LYS B   5       5.431  -9.020  -5.359  1.00  5.00 
ATOM     32  CA  LYS B   5       6.738  -8.737  -5.238  1.00  5.00 
ATOM     38  C   LYS B   5       6.857  -8.207  -3.954  1.00  5.00 
ATOM     39  O   LYS B   5       7.712  -8.601  -3.197  1.00  5.00 
ATOM     40  N   GLN B   6       6.002  -7.261  -3.618  1.00  5.00 
ATOM     41  CA  GLN B   6       6.189  -6.640  -2.393  1.00  5.00 
ATOM     47  C   GLN B   6       7.536  -6.015  -2.337  1.00  5.00 
ATOM     48  O   GLN B   6       7.895  -5.470  -1.311  1.00  5.00 
ATOM     49  N   GLU B   7       8.185  -5.961  -3.498  1.00  5.00 
ATOM     50  CA  GLU B   7       9.367  -5.444  -3.995  1.00  5.00 
ATOM     56  C   GLU B   7       8.747  -5.206  -5.242  1.00  5.00 
ATOM     57  O   GLU B   7       9.019  -5.823  -6.250  1.00  5.00 
ATOM     58  N   HIS B   8       7.808  -4.319  -5.143  1.00  5.00 
ATOM     59  CA  HIS B   8       6.974  -3.913  -6.160  1.00  5.00 
ATOM     66  C   HIS B   8       5.981  -3.987  -5.223  1.00  5.00 
ATOM     67  O   HIS B   8       5.886  -4.994  -4.566  1.00  5.00 
ATOM     68  N   PHE B   9       5.315  -2.902  -5.044  1.00  5.00 
ATOM     69  CA  PHE B   9       4.520  -2.997  -3.976  1.00  5.00 
ATOM     77  C   PHE B   9       5.549  -2.962  -2.935  1.00  5.00 
ATOM     78  O   PHE B   9       5.890  -3.918  -2.291  1.00  5.00 
ATOM     79  N   GLU B  10       6.114  -1.794  -2.874  1.00  5.00 
ATOM     80  CA  GLU B  10       7.168  -1.430  -2.050  1.00  5.00 
ATOM     86  C   GLU B  10       7.987  -1.079  -3.130  1.00  5.00 
ATOM     87  O   GLU B  10       9.093  -0.635  -2.986  1.00  5.00 
ATOM     88  N   LEU B  11       7.463  -1.392  -4.285  1.00  5.00 
ATOM     89  CA  LEU B  11       7.931  -0.755  -5.425  1.00  5.00 
ATOM     94  C   LEU B  11       6.614  -0.557  -5.911  1.00  5.00 
ATOM     95  O   LEU B  11       6.214  -1.001  -6.973  1.00  5.00 
ATOM     96  N   ASP B  12       5.870  -0.092  -4.940  1.00  5.00 
ATOM     97  CA  ASP B  12       4.597   0.384  -5.052  1.00  5.00 
ATOM    102  C   ASP B  12       4.203   0.131  -3.719  1.00  5.00 
ATOM    103  O   ASP B  12       3.368  -0.676  -3.390  1.00  5.00 
ATOM    104  N   GLN B  13       4.842   0.954  -2.934  1.00  5.00 
ATOM    105  CA  GLN B  13       4.969   0.979  -1.580  1.00  5.00 
ATOM    111  C   GLN B  13       6.344   1.319  -1.765  1.00  5.00 
ATOM    112  O   GLN B  13       7.201   1.089  -0.953  1.00  5.00 
ATOM    113  N   GLU B  14       6.576   1.781  -2.987  1.00  5.00 
ATOM    114  CA  GLU B  14       7.719   2.479  -3.403  1.00  5.00 
ATOM    120  C   GLU B  14       6.983   3.125  -4.422  1.00  5.00 
ATOM    121  O   GLU B  14       7.388   3.227  -5.558  1.00  5.00 
ATOM    122  N   TRP B  15       5.743   3.216  -4.037  1.00  5.00 
ATOM    123  CA  TRP B  15       4.884   4.176  -4.427  1.00  5.00 
ATOM    134  C   TRP B  15       4.484   4.257  -3.068  1.00  5.00 
ATOM    135  O   TRP B  15       5.174   3.783  -2.192  1.00  5.00 
ATOM    136  N   VAL B  16       3.351   4.908  -2.854  1.00  5.00 
ATOM    137  CA  VAL B  16       2.956   5.326  -1.590  1.00  5.00 
ATOM    141  C   VAL B  16       3.830   6.296  -1.998  1.00  5.00 
ATOM    142  O   VAL B  16       3.669   6.682  -3.144  1.00  5.00 
ATOM    143  N   GLU B  17       4.885   6.391  -1.191  1.00  5.00 
ATOM    144  CA  GLU B  17       6.079   7.128  -1.324  1.00  5.00 
ATOM    150  C   GLU B  17       6.354   7.181  -2.733  1.00  5.00 
ATOM    151  O   GLU B  17       6.132   6.258  -3.445  1.00  5.00 
ATOM    152  N   LEU B  18       6.853   8.287  -3.212  1.00  5.00 
ATOM    153  CA  LEU B  18       6.726   8.522  -4.601  1.00  5.00 
ATOM    158  C   LEU B  18       5.266   8.365  -4.883  1.00  5.00 
ATOM    159  O   LEU B  18       4.729   7.374  -5.337  1.00  5.00 
ATOM    160  N   MET B  19       4.565   9.406  -4.446  1.00  5.00 
ATOM    161  CA  MET B  19       3.190   9.487  -4.146  1.00  5.00 
ATOM    166  C   MET B  19       3.413   9.413  -2.706  1.00  5.00 
ATOM    167  O   MET B  19       4.442   8.912  -2.436  1.00  5.00 
ATOM    168  N   VAL B  20       2.658   9.864  -1.727  1.00  5.00 
ATOM    169  CA  VAL B  20       3.179  10.084  -0.428  1.00  5.00 
ATOM    173  C   VAL B  20       4.495  10.716  -0.609  1.00  5.00 
ATOM    174  O   VAL B  20       5.523  10.073  -0.490  1.00  5.00 
ATOM    175  N   GLU B  21       4.442  11.964  -1.006  1.00  5.00 
ATOM    176  CA  GLU B  21       5.487  12.660  -1.617  1.00  5.00 
ATOM    182  C   GLU B  21       4.850  12.787  -2.909  1.00  5.00 
ATOM    183  O   GLU B  21       4.389  11.789  -3.416  1.00  5.00 
ATOM    184  N   ALA B  22       4.815  13.961  -3.506  1.00  5.00 
ATOM    185  CA  ALA B  22       4.329  14.103  -4.820  1.00  5.00 
ATOM    187  C   ALA B  22       3.037  13.566  -4.894  1.00  5.00 
ATOM    188  O   ALA B  22       2.844  12.540  -5.530  1.00  5.00 
ATOM    189  N   LYS B  23       2.144  14.296  -4.254  1.00  5.00 
ATOM    190  CA  LYS B  23       0.782  14.013  -4.087  1.00  5.00 
ATOM    196  C   LYS B  23       0.484  14.604  -2.781  1.00  5.00 
ATOM    197  O   LYS B  23      -0.374  14.124  -2.062  1.00  5.00 
ATOM    198  N   GLU B  24       1.459  15.414  -2.380  1.00  5.00 
ATOM    199  CA  GLU B  24       1.499  16.264  -1.257  1.00  5.00 
ATOM    205  C   GLU B  24       2.435  17.155  -1.883  1.00  5.00 
ATOM    206  O   GLU B  24       2.756  18.223  -1.417  1.00  5.00 
ATOM    207  N   ALA B  25       3.031  16.617  -2.936  1.00  5.00 
ATOM    208  CA  ALA B  25       3.965  17.387  -3.632  1.00  5.00 
ATOM    210  C   ALA B  25       3.281  17.446  -4.900  1.00  5.00 
ATOM    211  O   ALA B  25       3.926  17.472  -5.936  1.00  5.00 
ATOM    212  N   ASN B  26       1.941  17.390  -4.773  1.00  5.00 
ATOM    213  CA  ASN B  26       0.917  17.398  -5.754  1.00  5.00 
ATOM    218  C   ASN B  26      -0.148  16.640  -5.066  1.00  5.00 
ATOM    219  O   ASN B  26      -0.319  16.946  -3.890  1.00  5.00 
ATOM    220  N   ILE B  27      -0.897  15.738  -5.763  1.00  5.00 
ATOM    221  CA  ILE B  27      -1.812  14.783  -5.193  1.00  5.00 
ATOM    226  C   ILE B  27      -2.119  13.875  -6.330  1.00  5.00 
ATOM    227  O   ILE B  27      -1.327  13.779  -7.265  1.00  5.00 
ATOM    228  N   SER B  28      -3.297  13.233  -6.266  1.00  5.00 
ATOM    229  CA  SER B  28      -3.816  12.265  -7.134  1.00  5.00 
ATOM    232  C   SER B  28      -4.127  11.180  -6.219  1.00  5.00 
ATOM    233  O   SER B  28      -3.672  11.128  -5.081  1.00  5.00 
ATOM    234  N   PRO B  29      -5.035  10.439  -6.744  1.00  5.00 
ATOM    235  CA  PRO B  29      -5.325   9.186  -6.219  1.00  5.00 
ATOM    239  C   PRO B  29      -5.085   8.737  -7.570  1.00  5.00 
ATOM    240  O   PRO B  29      -4.324   9.397  -8.281  1.00  5.00 
ATOM    241  N   GLU B  30      -5.844   7.723  -7.932  1.00  5.00 
ATOM    242  CA  GLU B  30      -5.803   7.134  -9.193  1.00  5.00 
ATOM    248  C   GLU B  30      -4.415   6.854  -9.448  1.00  5.00 
ATOM    249  O   GLU B  30      -3.712   7.698 -10.006  1.00  5.00 
ATOM    250  N   GLU B  31      -4.049   5.596  -9.107  1.00  5.00 
ATOM    251  CA  GLU B  31      -2.780   5.110  -9.405  1.00  5.00 
ATOM    257  C   GLU B  31      -2.213   5.802  -8.357  1.00  5.00 
ATOM    258  O   GLU B  31      -1.853   6.949  -8.500  1.00  5.00 
ATOM    259  N   ILE B  32      -2.130   5.016  -7.307  1.00  5.00 
ATOM    260  CA  ILE B  32      -2.320   5.547  -6.070  1.00  5.00 
ATOM    265  C   ILE B  32      -3.738   5.507  -6.269  1.00  5.00 
ATOM    266  O   ILE B  32      -4.311   6.554  -6.138  1.00  5.00 
ATOM    267  N   ARG B  33      -4.277   4.331  -6.626  1.00  5.00 
ATOM    268  CA  ARG B  33      -5.652   4.097  -6.786  1.00  5.00 
ATOM    276  C   ARG B  33      -5.574   3.475  -7.982  1.00  5.00 
ATOM    277  O   ARG B  33      -6.027   3.947  -9.009  1.00  5.00 
ATOM    278  N   LYS B  34      -5.065   2.320  -7.727  1.00  5.00 
ATOM    279  CA  LYS B  34      -4.330   1.677  -8.665  1.00  5.00 
ATOM    285  C   LYS B  34      -3.140   1.913  -7.945  1.00  5.00 
ATOM    286  O   LYS B  34      -2.262   2.641  -8.359  1.00  5.00 
ATOM    287  N   TYR B  35      -3.172   1.393  -6.759  1.00  5.00 
ATOM    288  CA  TYR B  35      -2.025   1.403  -6.038  1.00  5.00 
ATOM    297  C   TYR B  35      -2.761   0.997  -4.953  1.00  5.00 
ATOM    298  O   TYR B  35      -2.276   0.477  -4.001  1.00  5.00 
ATOM    299  N   LEU B  36      -4.025   1.256  -5.050  1.00  5.00 
ATOM    300  CA  LEU B  36      -4.590   1.046  -3.824  1.00  5.00 
ATOM    305  C   LEU B  36      -5.438   0.115  -4.273  1.00  5.00 
ATOM    306  O   LEU B  36      -6.029  -0.677  -3.591  1.00  5.00 
ATOM    307  N   LEU B  37      -5.616   0.365  -5.514  1.00  5.00 
ATOM    308  CA  LEU B  37      -6.372  -0.478  -6.238  1.00  5.00 
ATOM    313  C   LEU B  37      -5.280  -1.101  -6.888  1.00  5.00 
ATOM    314  O   LEU B  37      -4.980  -0.885  -8.053  1.00  5.00 
ATOM    315  N   LEU B  38      -4.659  -1.925  -6.044  1.00  5.00 
ATOM    316  CA  LEU B  38      -3.420  -2.397  -6.374  1.00  5.00 
ATOM    321  C   LEU B  38      -2.864  -2.266  -5.055  1.00  5.00 
ATOM    322  O   LEU B  38      -1.756  -1.812  -4.849  1.00  5.00 
ATOM    323  N   ASN B  39      -3.662  -2.599  -4.108  1.00  5.00 
ATOM    324  CA  ASN B  39      -3.300  -2.419  -2.798  1.00  5.00 
ATOM    329  C   ASN B  39      -4.486  -2.973  -2.469  1.00  5.00 
ATOM    330  O   ASN B  39      -5.078  -2.590  -1.495  1.00  5.00 
ATOM    331  N   LYS B  40      -4.901  -3.556  -3.551  1.00  5.00 
ATOM    332  CA  LYS B  40      -6.074  -4.158  -3.879  1.00  5.00 
ATOM    338  C   LYS B  40      -5.635  -4.553  -5.215  1.00  5.00 
ATOM    339  O   LYS B  40      -6.228  -4.297  -6.251  1.00  5.00 
ATOM    340  N   LYS B  41      -4.422  -5.072  -5.213  1.00  5.00 
ATOM    341  CA  LYS B  41      -3.950  -5.770  -6.335  1.00  5.00 
ATOM    347  C   LYS B  41      -4.288  -6.848  -5.539  1.00  5.00 
ATOM    348  O   LYS B  41      -5.432  -7.261  -5.486  1.00  5.00 
ATOM    349  N   SER B  42      -3.256  -7.122  -4.756  1.00  5.00 
ATOM    350  CA  SER B  42      -3.479  -7.833  -3.625  1.00  5.00 
ATOM    353  C   SER B  42      -3.916  -6.879  -2.657  1.00  5.00 
ATOM    354  O   SER B  42      -3.270  -5.906  -2.317  1.00  5.00 
ATOM    355  N   ALA B  43      -5.084  -7.181  -2.162  1.00  5.00 
ATOM    356  CA  ALA B  43      -5.480  -6.495  -1.027  1.00  5.00 
ATOM    358  C   ALA B  43      -5.404  -7.712  -0.416  1.00  5.00 
ATOM    359  O   ALA B  43      -5.154  -7.827   0.760  1.00  5.00 
ATOM    360  N   HIS B  44      -5.639  -8.606  -1.384  1.00  5.00 
ATOM    361  CA  HIS B  44      -5.618  -9.981  -1.477  1.00  5.00 
ATOM    368  C   HIS B  44      -4.561 -10.303  -2.427  1.00  5.00 
ATOM    369  O   HIS B  44      -4.622 -10.268  -3.649  1.00  5.00 
ATOM    370  N   PRO B  45      -3.652 -10.747  -1.645  1.00  5.00 
ATOM    371  CA  PRO B  45      -4.317 -10.914  -0.399  1.00  5.00 
ATOM    375  C   PRO B  45      -3.798 -10.188   0.735  1.00  5.00 
ATOM    376  O   PRO B  45      -4.544 -10.065   1.689  1.00  5.00 
ATOM    377  N   GLY B  46      -2.566  -9.724   0.731  1.00  5.00 
ATOM    378  CA  GLY B  46      -2.322  -9.126   1.983  1.00  5.00 
ATOM    379  C   GLY B  46      -1.928 -10.263   2.847  1.00  5.00 
ATOM    380  O   GLY B  46      -2.304 -11.399   2.593  1.00  5.00 
ATOM    381  N   PRO B  47      -1.144  -9.970   3.837  1.00  5.00 
ATOM    382  CA  PRO B  47      -0.810  -8.615   3.900  1.00  5.00 
ATOM    386  C   PRO B  47       0.596  -8.852   3.935  1.00  5.00 
ATOM    387  O   PRO B  47       1.061  -9.564   3.055  1.00  5.00 
ATOM    388  N   ALA B  48       1.269  -8.249   4.924  1.00  5.00 
ATOM    389  CA  ALA B  48       2.666  -8.306   5.021  1.00  5.00 
ATOM    391  C   ALA B  48       3.143  -7.411   3.982  1.00  5.00 
ATOM    392  O   ALA B  48       2.601  -7.431   2.884  1.00  5.00 
ATOM    393  N   ALA B  49       4.222  -6.675   4.289  1.00  5.00 
ATOM    394  CA  ALA B  49       4.585  -5.627   3.433  1.00  5.00 
ATOM    396  C   ALA B  49       3.407  -4.980   3.675  1.00  5.00 
ATOM    397  O   ALA B  49       3.266  -4.759   4.838  1.00  5.00 
ATOM    398  N   ARG B  50       2.562  -4.754   2.682  1.00  5.00 
ATOM    399  CA  ARG B  50       1.293  -4.216   2.793  1.00  5.00 
ATOM    407  C   ARG B  50       0.791  -5.129   3.755  1.00  5.00 
ATOM    408  O   ARG B  50       0.460  -6.210   3.361  1.00  5.00 
ATOM    409  N   SER B  51       0.735  -4.692   4.995  1.00  5.00 
ATOM    410  CA  SER B  51       0.466  -5.281   6.220  1.00  5.00 
ATOM    413  C   SER B  51       0.704  -4.060   6.841  1.00  5.00 
ATOM    414  O   SER B  51       0.031  -3.758   7.789  1.00  5.00 
ATOM    415  N   HIS B  52       1.560  -3.329   6.117  1.00  5.00 
ATOM    416  CA  HIS B  52       2.150  -2.073   6.181  1.00  5.00 
ATOM    423  C   HIS B  52       1.382  -1.458   5.164  1.00  5.00 
ATOM    424  O   HIS B  52       0.688  -2.218   4.505  1.00  5.00 
ATOM    425  N   THR B  53       1.583  -0.145   4.942  1.00  5.00 
ATOM    426  CA  THR B  53       0.819   0.554   4.003  1.00  5.00 
ATOM    430  C   THR B  53      -0.479   0.089   4.325  1.00  5.00 
ATOM    431  O   THR B  53      -1.118  -0.693   3.635  1.00  5.00 
ATOM    432  N   VAL B  54      -0.632   0.404   5.584  1.00  5.00 
ATOM    433  CA  VAL B  54      -1.482  -0.054   6.562  1.00  5.00 
ATOM    437  C   VAL B  54      -0.431  -0.398   7.543  1.00  5.00 
ATOM    438  O   VAL B  54      -0.468  -1.357   8.293  1.00  5.00 
ATOM    439  N   ASN B  55       0.608   0.418   7.390  1.00  5.00 
ATOM    440  CA  ASN B  55       1.776   0.789   8.124  1.00  5.00 
ATOM    445  C   ASN B  55       2.836   1.050   7.139  1.00  5.00 
ATOM    446  O   ASN B  55       3.735   0.244   6.951  1.00  5.00 
ATOM    447  N   PRO B  56       2.829   2.177   6.494  1.00  5.00 
ATOM    448  CA  PRO B  56       1.994   3.327   6.734  1.00  5.00 
ATOM    452  C   PRO B  56       0.527   3.126   6.820  1.00  5.00 
ATOM    453  O   PRO B  56       0.052   2.867   7.914  1.00  5.00 
ATOM    454  N   PHE B  57      -0.233   3.314   5.727  1.00  5.00 
ATOM    455  CA  PHE B  57      -1.637   3.026   5.791  1.00  5.00 
ATOM    463  C   PHE B  57      -2.049   2.606   4.392  1.00  5.00 
ATOM    464  O   PHE B  57      -3.231   2.211   4.216  1.00  5.00 
TER 
END 
