
PFRMAT TS
TARGET T0099
AUTHOR 3526-7872-4436
METHOD A hierarchical, generalized comparative modeling method has 
METHOD been applied to predict the tertiary structure. First, 
METHOD PROSPECTOR, a new threading algorithm, is used to select the 
METHOD template structure and to generate the initial alignment. Then, 
METHOD using the side chain, center of mass based lattice model 
METHOD (SICHO) of Kolinski and Skolnick [1], the gaps are filled in 
METHOD and the structure is refined in the neighborhood of the template 
METHOD fold; an early variant of this method has been described 
METHOD previously [2], but now the template is treated in a more 
METHOD permissive manner. From a series of folding/structure refinement 
METHOD simulations that employs parallel tempering to explore 
METHOD conformational space, the lowest energy structures are extracted 
METHOD and subjected to a two-part structure selection protocol. First, 
METHOD the structures are clustered, and the resulting clustered folds 
METHOD are selected to provide a set of predicted structures. In parallel, 
METHOD distance geometry is used to generate alternative representative 
METHOD structures. In addition the two lowest energy structures generated 
METHOD by the SICHO model are also included as models. All folds are 
METHOD locally relaxed using a more detailed off-lattice model comprised 
METHOD of the alpha carbons and a one or two center description of the 
METHOD side chains that depends on the side chain size. Atomic detail is 
METHOD then added and the resulting structures are reported.
METHOD 
METHOD [1] Kolinski A Skolnick, J. Assembly of protein structure from sparse 
METHOD experimental data. An efficient Monte Carlo Model. 
METHOD Proteins 1998;32: 475-494.
METHOD [2] Kolinski A, Rotkiewicz, P, Ilkowski, B Skolnick, J. A method for 
METHOD the improvement of threading-based protein models. Proteins 1999;37: 
METHOD 592-610.
MODEL  1
PARENT 1avzC
ATOM      1  N   GLU     1      -8.010   6.490  -6.068  1.00  5.00
ATOM      2  CA  GLU     1      -6.782   5.713  -6.223  1.00  5.00
ATOM      3  C   GLU     1      -5.517   6.532  -6.013  1.00  5.00
ATOM      4  O   GLU     1      -5.529   7.777  -6.185  1.00  5.00
ATOM      5  N   PHE     2      -4.563   5.908  -5.395  1.00  5.00
ATOM      6  CA  PHE     2      -3.354   6.559  -4.959  1.00  5.00
ATOM      7  C   PHE     2      -2.144   5.747  -5.360  1.00  5.00
ATOM      8  O   PHE     2      -2.159   4.495  -5.253  1.00  5.00
ATOM      9  N   ILE     3      -1.203   6.450  -5.924  1.00  5.00
ATOM     10  CA  ILE     3      -0.037   5.823  -6.481  1.00  5.00
ATOM     11  C   ILE     3       0.817   5.300  -5.350  1.00  5.00
ATOM     12  O   ILE     3       1.036   6.047  -4.366  1.00  5.00
ATOM     13  N   ALA     4       1.367   4.130  -5.579  1.00  5.00
ATOM     14  CA  ALA     4       2.369   3.515  -4.715  1.00  5.00
ATOM     15  C   ALA     4       3.775   3.800  -5.233  1.00  5.00
ATOM     16  O   ALA     4       3.931   4.261  -6.390  1.00  5.00
ATOM     17  N   ILE     5       4.849   3.430  -4.500  1.00  5.00
ATOM     18  CA  ILE     5       6.208   3.455  -5.049  1.00  5.00
ATOM     19  C   ILE     5       6.796   2.105  -4.604  1.00  5.00
ATOM     20  O   ILE     5       6.113   1.293  -3.986  1.00  5.00
ATOM     21  N   TYR     6       8.053   1.965  -5.008  1.00  5.00
ATOM     22  CA  TYR     6       8.666   0.665  -4.691  1.00  5.00
ATOM     23  C   TYR     6       8.972   0.683  -3.182  1.00  5.00
ATOM     24  O   TYR     6       9.368   1.702  -2.617  1.00  5.00
ATOM     25  N   ASP     7       8.855  -0.498  -2.576  1.00  5.00
ATOM     26  CA  ASP     7       9.258  -0.518  -1.160  1.00  5.00
ATOM     27  C   ASP     7       8.704  -1.787  -0.488  1.00  5.00
ATOM     28  O   ASP     7       8.138  -2.665  -1.133  1.00  5.00
ATOM     29  N   TYR     8       8.976  -1.789   0.805  1.00  5.00
ATOM     30  CA  TYR     8       8.458  -2.873   1.653  1.00  5.00
ATOM     31  C   TYR     8       7.252  -2.312   2.429  1.00  5.00
ATOM     32  O   TYR     8       7.360  -1.329   3.161  1.00  5.00
ATOM     33  N   LYS     9       7.057  -4.144   0.849  1.00  5.00
ATOM     34  CA  LYS     9       6.985  -5.530   1.329  1.00  5.00
ATOM     35  C   LYS     9       7.022  -5.469   2.876  1.00  5.00
ATOM     36  O   LYS     9       8.018  -5.028   3.458  1.00  5.00
ATOM     37  N   ALA    10       5.957  -5.922   3.535  1.00  5.00
ATOM     38  CA  ALA    10       5.909  -5.973   5.011  1.00  5.00
ATOM     39  C   ALA    10       6.106  -7.435   5.465  1.00  5.00
ATOM     40  O   ALA    10       6.170  -8.328   4.613  1.00  5.00
ATOM     41  N   GLU    11       6.265  -7.678   6.698  1.00  5.00
ATOM     42  CA  GLU    11       6.490  -9.034   7.239  1.00  5.00
ATOM     43  C   GLU    11       5.317  -9.621   8.034  1.00  5.00
ATOM     44  O   GLU    11       5.408 -10.727   8.598  1.00  5.00
ATOM     45  N   THR    12       4.239  -8.824   8.068  1.00  5.00
ATOM     46  CA  THR    12       2.976  -9.210   8.674  1.00  5.00
ATOM     47  C   THR    12       2.355 -10.350   7.868  1.00  5.00
ATOM     48  O   THR    12       2.770 -10.561   6.702  1.00  5.00
ATOM     49  N   GLU    13       1.418 -11.081   8.473  1.00  5.00
ATOM     50  CA  GLU    13       0.785 -12.247   7.825  1.00  5.00
ATOM     51  C   GLU    13      -0.183 -11.796   6.746  1.00  5.00
ATOM     52  O   GLU    13      -0.422 -12.560   5.771  1.00  5.00
ATOM     53  N   GLU    14      -0.607 -10.559   6.795  1.00  5.00
ATOM     54  CA  GLU    14      -1.282  -9.944   5.661  1.00  5.00
ATOM     55  C   GLU    14      -0.312  -8.825   5.275  1.00  5.00
ATOM     56  O   GLU    14      -0.289  -7.758   5.960  1.00  5.00
ATOM     57  N   ASP    15       0.586  -9.083   4.316  1.00  5.00
ATOM     58  CA  ASP    15       1.532  -8.027   3.901  1.00  5.00
ATOM     59  C   ASP    15       1.299  -7.689   2.428  1.00  5.00
ATOM     60  O   ASP    15       0.964  -8.542   1.598  1.00  5.00
ATOM     61  N   LEU    16       1.495  -6.292   2.359  1.00  5.00
ATOM     62  CA  LEU    16       1.340  -5.724   0.948  1.00  5.00
ATOM     63  C   LEU    16       2.646  -5.875   0.195  1.00  5.00
ATOM     64  O   LEU    16       3.746  -5.830   0.756  1.00  5.00
ATOM     65  N   THR    17       2.601  -5.992  -1.014  1.00  5.00
ATOM     66  CA  THR    17       3.864  -6.245  -1.760  1.00  5.00
ATOM     67  C   THR    17       4.646  -4.911  -1.842  1.00  5.00
ATOM     68  O   THR    17       5.888  -4.885  -1.809  1.00  5.00
ATOM     69  N   ILE    18       3.909  -3.853  -1.983  1.00  5.00
ATOM     70  CA  ILE    18       4.488  -2.475  -2.030  1.00  5.00
ATOM     71  C   ILE    18       5.591  -2.358  -3.113  1.00  5.00
ATOM     72  O   ILE    18       6.729  -2.044  -2.843  1.00  5.00
ATOM     73  N   LYS    19       5.295  -2.677  -4.189  1.00  5.00
ATOM     74  CA  LYS    19       6.126  -2.675  -5.378  1.00  5.00
ATOM     75  C   LYS    19       5.898  -1.383  -6.197  1.00  5.00
ATOM     76  O   LYS    19       5.110  -0.603  -5.691  1.00  5.00
ATOM     77  N   LYS    20       6.618  -1.225  -7.221  1.00  5.00
ATOM     78  CA  LYS    20       6.631   0.045  -7.919  1.00  5.00
ATOM     79  C   LYS    20       5.381   0.303  -8.736  1.00  5.00
ATOM     80  O   LYS    20       4.937  -0.571  -9.487  1.00  5.00
ATOM     81  N   GLY    21       4.775   1.422  -8.459  1.00  5.00
ATOM     82  CA  GLY    21       3.596   1.970  -9.161  1.00  5.00
ATOM     83  C   GLY    21       2.574   0.869  -9.402  1.00  5.00
ATOM     84  O   GLY    21       2.125   0.759 -10.567  1.00  5.00
ATOM     85  N   GLU    22       2.268  -0.022  -8.380  1.00  5.00
ATOM     86  CA  GLU    22       1.171  -0.976  -8.576  1.00  5.00
ATOM     87  C   GLU    22      -0.235  -0.355  -8.611  1.00  5.00
ATOM     88  O   GLU    22      -1.120  -0.864  -9.302  1.00  5.00
ATOM     89  N   LYS    23      -0.250   0.709  -7.816  1.00  5.00
ATOM     90  CA  LYS    23      -1.527   1.350  -7.542  1.00  5.00
ATOM     91  C   LYS    23      -2.076   0.842  -6.222  1.00  5.00
ATOM     92  O   LYS    23      -1.783  -0.322  -5.851  1.00  5.00
ATOM     93  N   LEU    24      -2.606   1.734  -5.689  1.00  5.00
ATOM     94  CA  LEU    24      -3.195   1.376  -4.358  1.00  5.00
ATOM     95  C   LEU    24      -4.593   1.936  -4.249  1.00  5.00
ATOM     96  O   LEU    24      -5.042   2.820  -5.041  1.00  5.00
ATOM     97  N   GLU    25      -5.253   1.443  -3.280  1.00  5.00
ATOM     98  CA  GLU    25      -6.654   1.725  -3.005  1.00  5.00
ATOM     99  C   GLU    25      -6.853   2.099  -1.541  1.00  5.00
ATOM    100  O   GLU    25      -7.393   1.239  -0.792  1.00  5.00
ATOM    101  N   ILE    26      -6.356   3.267  -1.109  1.00  5.00
ATOM    102  CA  ILE    26      -6.024   3.572   0.310  1.00  5.00
ATOM    103  C   ILE    26      -7.160   3.653   1.314  1.00  5.00
ATOM    104  O   ILE    26      -8.316   4.047   1.007  1.00  5.00
ATOM    105  N   ILE    27      -6.668   3.115   2.364  1.00  5.00
ATOM    106  CA  ILE    27      -7.512   3.319   3.551  1.00  5.00
ATOM    107  C   ILE    27      -6.598   3.763   4.701  1.00  5.00
ATOM    108  O   ILE    27      -5.655   3.011   5.029  1.00  5.00
ATOM    109  N   GLU    28      -6.765   4.957   5.184  1.00  5.00
ATOM    110  CA  GLU    28      -5.819   5.522   6.232  1.00  5.00
ATOM    111  C   GLU    28      -6.644   5.765   7.448  1.00  5.00
ATOM    112  O   GLU    28      -7.659   6.431   7.265  1.00  5.00
ATOM    113  N   LYS    29      -6.332   5.226   8.630  1.00  5.00
ATOM    114  CA  LYS    29      -7.232   5.147   9.811  1.00  5.00
ATOM    115  C   LYS    29      -6.555   5.389  11.158  1.00  5.00
ATOM    116  O   LYS    29      -7.095   6.106  12.065  1.00  5.00
ATOM    117  N   GLU    30      -5.392   4.783  11.386  1.00  5.00
ATOM    118  CA  GLU    30      -4.808   4.905  12.767  1.00  5.00
ATOM    119  C   GLU    30      -3.294   5.002  12.645  1.00  5.00
ATOM    120  O   GLU    30      -2.614   4.024  12.282  1.00  5.00
ATOM    121  N   GLY    31      -3.006   6.248  12.880  1.00  5.00
ATOM    122  CA  GLY    31      -1.567   6.644  12.884  1.00  5.00
ATOM    123  C   GLY    31      -0.995   6.850  11.506  1.00  5.00
ATOM    124  O   GLY    31      -1.593   7.598  10.689  1.00  5.00
ATOM    125  N   ASP    32       0.163   6.237  11.223  1.00  5.00
ATOM    126  CA  ASP    32       0.818   6.398   9.917  1.00  5.00
ATOM    127  C   ASP    32       0.663   5.171   9.051  1.00  5.00
ATOM    128  O   ASP    32       0.847   4.022   9.558  1.00  5.00
ATOM    129  N   TRP    33       0.370   5.349   7.820  1.00  5.00
ATOM    130  CA  TRP    33       0.233   4.263   6.840  1.00  5.00
ATOM    131  C   TRP    33      -0.177   2.833   7.196  1.00  5.00
ATOM    132  O   TRP    33       0.645   2.028   7.683  1.00  5.00
ATOM    133  N   TRP    34      -1.618   2.567   6.993  1.00  5.00
ATOM    134  CA  TRP    34      -2.111   1.214   7.287  1.00  5.00
ATOM    135  C   TRP    34      -3.461   1.144   6.565  1.00  5.00
ATOM    136  O   TRP    34      -4.076   2.168   6.243  1.00  5.00
ATOM    137  N   LYS    35      -3.923  -0.055   6.232  1.00  5.00
ATOM    138  CA  LYS    35      -5.182  -0.378   5.549  1.00  5.00
ATOM    139  C   LYS    35      -5.100   0.023   4.075  1.00  5.00
ATOM    140  O   LYS    35      -5.810   0.944   3.618  1.00  5.00
ATOM    141  N   ALA    36      -4.236  -0.689   3.368  1.00  5.00
ATOM    142  CA  ALA    36      -4.008  -0.480   1.933  1.00  5.00
ATOM    143  C   ALA    36      -4.681  -1.630   1.181  1.00  5.00
ATOM    144  O   ALA    36      -4.883  -2.732   1.737  1.00  5.00
ATOM    145  N   LYS    37      -5.357  -1.429   0.054  1.00  5.00
ATOM    146  CA  LYS    37      -5.299  -2.394  -1.055  1.00  5.00
ATOM    147  C   LYS    37      -4.508  -2.266  -2.360  1.00  5.00
ATOM    148  O   LYS    37      -4.569  -1.233  -3.039  1.00  5.00
ATOM    149  N   ALA    38      -3.623  -3.272  -2.685  1.00  5.00
ATOM    150  CA  ALA    38      -2.921  -3.159  -3.955  1.00  5.00
ATOM    151  C   ALA    38      -3.889  -3.266  -5.136  1.00  5.00
ATOM    152  O   ALA    38      -4.524  -4.335  -5.327  1.00  5.00
ATOM    153  N   ILE    39      -4.108  -2.161  -5.815  1.00  5.00
ATOM    154  CA  ILE    39      -5.056  -2.126  -6.941  1.00  5.00
ATOM    155  C   ILE    39      -4.576  -2.831  -8.210  1.00  5.00
ATOM    156  O   ILE    39      -5.377  -2.975  -9.167  1.00  5.00
ATOM    157  N   GLY    40      -3.337  -3.281  -8.221  1.00  5.00
ATOM    158  CA  GLY    40      -2.768  -4.000  -9.354  1.00  5.00
ATOM    159  C   GLY    40      -2.646  -5.493  -9.094  1.00  5.00
ATOM    160  O   GLY    40      -2.359  -6.244 -10.062  1.00  5.00
ATOM    161  N   SER    41      -2.824  -5.856  -7.970  1.00  5.00
ATOM    162  CA  SER    41      -2.764  -7.285  -7.651  1.00  5.00
ATOM    163  C   SER    41      -3.950  -8.015  -7.025  1.00  5.00
ATOM    164  O   SER    41      -3.996  -9.256  -7.002  1.00  5.00
ATOM    165  N   GLY    42      -5.058  -7.254  -6.651  1.00  5.00
ATOM    166  CA  GLY    42      -6.270  -7.956  -6.210  1.00  5.00
ATOM    167  C   GLY    42      -6.203  -8.393  -4.737  1.00  5.00
ATOM    168  O   GLY    42      -6.996  -9.222  -4.294  1.00  5.00
ATOM    169  N   GLU    43      -5.245  -7.776  -4.058  1.00  5.00
ATOM    170  CA  GLU    43      -4.966  -8.090  -2.655  1.00  5.00
ATOM    171  C   GLU    43      -5.314  -7.009  -1.625  1.00  5.00
ATOM    172  O   GLU    43      -5.223  -5.817  -1.910  1.00  5.00
ATOM    173  N   ILE    44      -5.727  -7.557  -0.499  1.00  5.00
ATOM    174  CA  ILE    44      -5.929  -6.735   0.711  1.00  5.00
ATOM    175  C   ILE    44      -4.579  -6.588   1.443  1.00  5.00
ATOM    176  O   ILE    44      -4.210  -7.462   2.240  1.00  5.00
ATOM    177  N   GLY    45      -3.913  -5.476   1.136  1.00  5.00
ATOM    178  CA  GLY    45      -2.610  -5.202   1.787  1.00  5.00
ATOM    179  C   GLY    45      -2.774  -4.352   3.036  1.00  5.00
ATOM    180  O   GLY    45      -3.841  -3.761   3.279  1.00  5.00
ATOM    181  N   TYR    46      -1.957  -4.367   3.644  1.00  5.00
ATOM    182  CA  TYR    46      -1.737  -3.473   4.817  1.00  5.00
ATOM    183  C   TYR    46      -0.388  -2.769   4.512  1.00  5.00
ATOM    184  O   TYR    46       0.637  -3.448   4.364  1.00  5.00
ATOM    185  N   ILE    47      -0.364  -1.480   4.423  1.00  5.00
ATOM    186  CA  ILE    47       0.738  -0.642   3.920  1.00  5.00
ATOM    187  C   ILE    47       1.702  -0.415   5.088  1.00  5.00
ATOM    188  O   ILE    47       1.297  -0.406   6.261  1.00  5.00
ATOM    189  N   PRO    48       2.965  -0.379   4.871  1.00  5.00
ATOM    190  CA  PRO    48       4.005  -0.008   5.892  1.00  5.00
ATOM    191  C   PRO    48       3.950   1.531   6.057  1.00  5.00
ATOM    192  O   PRO    48       3.180   2.216   5.360  1.00  5.00
ATOM    193  N   ALA    49       4.786   2.019   6.869  1.00  5.00
ATOM    194  CA  ALA    49       4.815   3.428   7.221  1.00  5.00
ATOM    195  C   ALA    49       4.971   4.345   6.067  1.00  5.00
ATOM    196  O   ALA    49       4.351   5.421   6.068  1.00  5.00
ATOM    197  N   ASN    50       5.892   3.981   5.139  1.00  5.00
ATOM    198  CA  ASN    50       6.206   4.929   4.033  1.00  5.00
ATOM    199  C   ASN    50       5.820   4.364   2.680  1.00  5.00
ATOM    200  O   ASN    50       5.651   3.161   2.469  1.00  5.00
ATOM    201  N   TYR    51       5.659   5.253   1.856  1.00  5.00
ATOM    202  CA  TYR    51       5.137   4.910   0.552  1.00  5.00
ATOM    203  C   TYR    51       3.945   5.781   0.203  1.00  5.00
ATOM    204  O   TYR    51       3.960   7.008   0.494  1.00  5.00
ATOM    205  N   ILE    52       3.311   5.165  -0.774  1.00  5.00
ATOM    206  CA  ILE    52       2.007   5.695  -1.206  1.00  5.00
ATOM    207  C   ILE    52       2.061   7.065  -1.878  1.00  5.00
ATOM    208  O   ILE    52       1.279   7.956  -1.502  1.00  5.00
ATOM    209  N   ALA    53       2.959   7.255  -2.831  1.00  5.00
ATOM    210  CA  ALA    53       3.014   8.538  -3.558  1.00  5.00
ATOM    211  C   ALA    53       1.688   8.767  -4.285  1.00  5.00
ATOM    212  O   ALA    53       1.117   7.849  -4.891  1.00  5.00
ATOM    213  N   ALA    54       1.119   9.917  -4.212  1.00  5.00
ATOM    214  CA  ALA    54      -0.213  10.096  -4.782  1.00  5.00
ATOM    215  C   ALA    54      -0.374  10.953  -6.036  1.00  5.00
ATOM    216  O   ALA    54      -0.089  12.152  -6.011  1.00  5.00
ATOM    217  N   ALA    55      -0.829  10.315  -7.089  1.00  5.00
ATOM    218  CA  ALA    55      -1.134  11.042  -8.328  1.00  5.00
ATOM    219  C   ALA    55      -2.555  10.873  -8.867  1.00  5.00
ATOM    220  O   ALA    55      -3.217   9.858  -8.602  1.00  5.00
ATOM    221  N   GLU    56      -3.002  11.866  -9.617  1.00  5.00
ATOM    222  CA  GLU    56      -4.380  11.869 -10.126  1.00  5.00
ATOM    223  C   GLU    56      -4.369  12.152 -11.629  1.00  5.00
ATOM    224  O   GLU    56      -3.517  12.899 -12.129  1.00  5.00
TER
END


