
PFRMAT TS
TARGET T0099
AUTHOR 7282-4954-1811
METHOD    
METHOD    C_a-only prediction by "Dill-Ken" server using
METHOD    ENTSP -- Elastic Net prediction of protein structures via
METHOD             a Traveling Salesman Problem analogue method
METHOD    
METHOD    
METHOD    Predicts backbone topology and basic tertiary structure
METHOD    using the elastic net combinatorial optimization method [1]
METHOD    applied in a novel fashion to approximate the internal free
METHOD    energy landscape of a protein C_a chain, as represented by a
METHOD    simple residue-residue energy function E_stat incorporating
METHOD    a knowledge-based statistical contact potential [2], bond
METHOD    length restraint E_bond, centrosymmetric hydrophobic
METHOD    burial/polar expulsion term E_HP, and formation of predicted
METHOD    secondary structure E_2nd, as provided by the PHD algorithm
METHOD    [3] on the PredictProtein server [4].
METHOD    
METHOD    
METHOD    Terms of the potential take the form of harmonic oscillators:
METHOD    
METHOD    E = 0.5 * a * (r - r_0)^2
METHOD    
METHOD    Scaling parameters used are the following:
METHOD    
METHOD                  a               r0
METHOD    ------------------------------------
METHOD    stat         0.09 (max.)      0.0
METHOD    bond         6.0              3.8
METHOD    HP           0.1              N/A
METHOD    2nd          0.5              varies
METHOD    
METHOD    
METHOD    Full backbone construction created by PULCHRA version 0.81 [5].
METHOD    
METHOD    
METHOD    References:
METHOD    
METHOD    [1] Durbin & Willshaw, Nature 1:348-358 (1989).
METHOD    [2] Thomas & Dill, Proc. Nat. Acad. Sci. USA 93:11628-11633 (1996).
METHOD    [3] B. Rost & C. Sander, J. Mol. Biol. 232:584-599 (1993);
METHOD        Proteins, 1994, 19, 55-77.
METHOD    [4] B. Rost, Meth. in Enzym., 1996, 266:525-539 (1996).
METHOD        http://www.sdsc.edu/predictprotein/
METHOD    [5] written by Piotr Rotkiewicz (piotr@pirx.com)
METHOD    
MODEL  2  REFINED
PARENT N/A
ATOM      1  N   GLU     1       8.097  -5.840   7.342  1.00  0.00
ATOM      2  CA  GLU     1       6.951  -5.107   7.315  1.00  0.00
ATOM      3  C   GLU     1       6.472  -4.528   6.000  1.00  0.00
ATOM      4  O   GLU     1       7.067  -4.697   4.999  1.00  0.00
ATOM      5  N   PHE     2       5.326  -3.795   5.973  1.00  0.00
ATOM      6  CA  PHE     2       4.771  -3.181   4.717  1.00  0.00
ATOM      7  C   PHE     2       4.216  -2.733   3.381  1.00  0.00
ATOM      8  O   PHE     2       4.798  -2.925   2.376  1.00  0.00
ATOM      9  N   ILE     3       3.016  -2.093   3.339  1.00  0.00
ATOM     10  CA  ILE     3       2.515  -1.697   2.207  1.00  0.00
ATOM     11  C   ILE     3       1.487  -0.597   2.038  1.00  0.00
ATOM     12  O   ILE     3       0.475  -0.603   2.639  1.00  0.00
ATOM     13  N   ALA     4       1.737   0.421   1.171  1.00  0.00
ATOM     14  CA  ALA     4       1.043   1.060   1.130  1.00  0.00
ATOM     15  C   ALA     4      -0.278   1.603   1.634  1.00  0.00
ATOM     16  O   ALA     4      -1.303   1.117   1.320  1.00  0.00
ATOM     17  N   ILE     5      -0.282   2.677   2.469  1.00  0.00
ATOM     18  CA  ILE     5      -1.163   2.959   2.743  1.00  0.00
ATOM     19  C   ILE     5      -1.674   3.258   4.137  1.00  0.00
ATOM     20  O   ILE     5      -2.221   2.439   4.781  1.00  0.00
ATOM     21  N   TYR     6      -1.498   4.502   4.659  1.00  0.00
ATOM     22  CA  TYR     6      -1.938   4.816   5.901  1.00  0.00
ATOM     23  C   TYR     6      -1.677   5.476   7.240  1.00  0.00
ATOM     24  O   TYR     6      -0.840   5.082   7.967  1.00  0.00
ATOM     25  N   ASP     7      -2.428   6.548   7.611  1.00  0.00
ATOM     26  CA  ASP     7      -2.250   7.320   8.983  1.00  0.00
ATOM     27  C   ASP     7      -1.583   7.768   7.699  1.00  0.00
ATOM     28  O   ASP     7      -2.144   8.447   6.918  1.00  0.00
ATOM     29  N   TYR     8      -0.306   7.377   7.441  1.00  0.00
ATOM     30  CA  TYR     8       0.235   7.737   6.406  1.00  0.00
ATOM     31  C   TYR     8       0.687   9.122   5.991  1.00  0.00
ATOM     32  O   TYR     8       0.033   9.796   5.282  1.00  0.00
ATOM     33  N   LYS     9       1.876   9.599   6.449  1.00  0.00
ATOM     34  CA  LYS     9       2.382  10.921   6.096  1.00  0.00
ATOM     35  C   LYS     9       1.671  10.775   4.766  1.00  0.00
ATOM     36  O   LYS     9       0.666  11.344   4.540  1.00  0.00
ATOM     37  N   ALA    10       2.206   9.967   3.811  1.00  0.00
ATOM     38  CA  ALA    10       1.508   9.665   2.168  1.00  0.00
ATOM     39  C   ALA    10       0.709  10.095   0.955  1.00  0.00
ATOM     40  O   ALA    10      -0.466  10.150   0.980  1.00  0.00
ATOM     41  N   GLU    11       1.364  10.426  -0.190  1.00  0.00
ATOM     42  CA  GLU    11       0.596  10.952  -1.707  1.00  0.00
ATOM     43  C   GLU    11       0.960  10.991  -3.177  1.00  0.00
ATOM     44  O   GLU    11       2.011  11.376  -3.540  1.00  0.00
ATOM     45  N   THR    12       0.053  10.571  -4.099  1.00  0.00
ATOM     46  CA  THR    12       0.318  10.566  -5.651  1.00  0.00
ATOM     47  C   THR    12       0.780  11.028  -7.017  1.00  0.00
ATOM     48  O   THR    12       0.696  12.155  -7.347  1.00  0.00
ATOM     49  N   GLU    13       1.305  10.122  -7.885  1.00  0.00
ATOM     50  CA  GLU    13       1.738  10.488  -9.132  1.00  0.00
ATOM     51  C   GLU    13       3.181  10.032  -9.194  1.00  0.00
ATOM     52  O   GLU    13       4.070  10.768  -8.964  1.00  0.00
ATOM     53  N   GLU    14       3.458   8.742  -9.524  1.00  0.00
ATOM     54  CA  GLU    14       4.756   8.272  -9.596  1.00  0.00
ATOM     55  C   GLU    14       3.489   7.499  -9.293  1.00  0.00
ATOM     56  O   GLU    14       2.857   6.994 -10.148  1.00  0.00
ATOM     57  N   ASP    15       3.071   7.384  -8.004  1.00  0.00
ATOM     58  CA  ASP    15       2.287   6.894  -7.918  1.00  0.00
ATOM     59  C   ASP    15       1.891   5.573  -7.291  1.00  0.00
ATOM     60  O   ASP    15       1.711   4.611  -7.944  1.00  0.00
ATOM     61  N   LEU    16       1.738   5.496  -5.941  1.00  0.00
ATOM     62  CA  LEU    16       1.282   4.046  -5.042  1.00  0.00
ATOM     63  C   LEU    16       2.704   4.470  -4.736  1.00  0.00
ATOM     64  O   LEU    16       2.939   5.302  -3.937  1.00  0.00
ATOM     65  N   THR    17       3.733   3.877  -5.399  1.00  0.00
ATOM     66  CA  THR    17       4.579   4.203  -5.145  1.00  0.00
ATOM     67  C   THR    17       4.508   2.963  -6.012  1.00  0.00
ATOM     68  O   THR    17       4.450   3.035  -7.186  1.00  0.00
ATOM     69  N   ILE    18       4.512   1.737  -5.423  1.00  0.00
ATOM     70  CA  ILE    18       4.459   0.844  -6.089  1.00  0.00
ATOM     71  C   ILE    18       5.344   0.573  -7.289  1.00  0.00
ATOM     72  O   ILE    18       4.978   0.794  -8.385  1.00  0.00
ATOM     73  N   LYS    19       6.590   0.063  -7.095  1.00  0.00
ATOM     74  CA  LYS    19       8.003  -0.401  -8.544  1.00  0.00
ATOM     75  C   LYS    19       9.415  -0.283  -9.079  1.00  0.00
ATOM     76  O   LYS    19       9.872   0.757  -9.387  1.00  0.00
ATOM     77  N   LYS    20      10.174  -1.405  -9.209  1.00  0.00
ATOM     78  CA  LYS    20      11.434  -1.346  -9.680  1.00  0.00
ATOM     79  C   LYS    20      11.237  -2.794  -9.279  1.00  0.00
ATOM     80  O   LYS    20      10.784  -3.583 -10.026  1.00  0.00
ATOM     81  N   GLY    21      11.591  -3.192  -8.028  1.00  0.00
ATOM     82  CA  GLY    21      11.433  -4.595  -7.546  1.00  0.00
ATOM     83  C   GLY    21      11.136  -5.530  -6.392  1.00  0.00
ATOM     84  O   GLY    21      10.880  -5.121  -5.318  1.00  0.00
ATOM     85  N   GLU    22      11.164  -6.874  -6.599  1.00  0.00
ATOM     86  CA  GLU    22      10.850  -8.075  -5.396  1.00  0.00
ATOM     87  C   GLU    22       9.473  -8.074  -4.764  1.00  0.00
ATOM     88  O   GLU    22       9.263  -7.520  -3.747  1.00  0.00
ATOM     89  N   LYS    23       8.456  -8.730  -5.384  1.00  0.00
ATOM     90  CA  LYS    23       7.003  -8.795  -4.826  1.00  0.00
ATOM     91  C   LYS    23       6.009  -8.204  -3.848  1.00  0.00
ATOM     92  O   LYS    23       6.047  -8.461  -2.700  1.00  0.00
ATOM     93  N   LEU    24       5.049  -7.356  -4.305  1.00  0.00
ATOM     94  CA  LEU    24       3.981  -6.693  -3.394  1.00  0.00
ATOM     95  C   LEU    24       3.515  -7.983  -4.037  1.00  0.00
ATOM     96  O   LEU    24       3.281  -8.941  -3.395  1.00  0.00
ATOM     97  N   GLU    25       3.362  -8.037  -5.387  1.00  0.00
ATOM     98  CA  GLU    25       2.916  -9.243  -6.085  1.00  0.00
ATOM     99  C   GLU    25       2.934  -7.746  -5.856  1.00  0.00
ATOM    100  O   GLU    25       3.603  -7.031  -6.509  1.00  0.00
ATOM    101  N   ILE    26       2.159  -7.213  -4.873  1.00  0.00
ATOM    102  CA  ILE    26       2.036  -5.422  -4.433  1.00  0.00
ATOM    103  C   ILE    26       0.787  -4.690  -4.880  1.00  0.00
ATOM    104  O   ILE    26       0.746  -4.113  -5.904  1.00  0.00
ATOM    105  N   ILE    27      -0.313  -4.700  -4.080  1.00  0.00
ATOM    106  CA  ILE    27      -0.997  -4.238  -4.437  1.00  0.00
ATOM    107  C   ILE    27      -1.917  -4.562  -5.596  1.00  0.00
ATOM    108  O   ILE    27      -1.834  -3.997  -6.625  1.00  0.00
ATOM    109  N   GLU    28      -2.861  -5.530  -5.446  1.00  0.00
ATOM    110  CA  GLU    28      -3.924  -5.984  -6.617  1.00  0.00
ATOM    111  C   GLU    28      -4.249  -4.801  -7.506  1.00  0.00
ATOM    112  O   GLU    28      -3.666  -4.607  -8.510  1.00  0.00
ATOM    113  N   LYS    29      -5.237  -3.942  -7.136  1.00  0.00
ATOM    114  CA  LYS    29      -5.646  -2.713  -7.964  1.00  0.00
ATOM    115  C   LYS    29      -6.774  -1.791  -8.381  1.00  0.00
ATOM    116  O   LYS    29      -7.776  -2.211  -8.834  1.00  0.00
ATOM    117  N   GLU    30      -6.627  -0.448  -8.228  1.00  0.00
ATOM    118  CA  GLU    30      -7.608   0.415  -8.586  1.00  0.00
ATOM    119  C   GLU    30      -8.011   0.550  -7.132  1.00  0.00
ATOM    120  O   GLU    30      -7.345   1.138  -6.361  1.00  0.00
ATOM    121  N   GLY    31      -9.170  -0.022  -6.707  1.00  0.00
ATOM    122  CA  GLY    31      -9.809   0.031  -5.032  1.00  0.00
ATOM    123  C   GLY    31     -10.435  -0.798  -3.930  1.00  0.00
ATOM    124  O   GLY    31     -11.105  -1.736  -4.169  1.00  0.00
ATOM    125  N   ASP    32     -10.220  -0.452  -2.632  1.00  0.00
ATOM    126  CA  ASP    32     -10.877  -1.311  -1.189  1.00  0.00
ATOM    127  C   ASP    32     -10.048  -2.359  -0.474  1.00  0.00
ATOM    128  O   ASP    32     -10.131  -3.500  -0.747  1.00  0.00
ATOM    129  N   TRP    33      -9.189  -1.972   0.506  1.00  0.00
ATOM    130  CA  TRP    33      -8.358  -2.917   1.240  1.00  0.00
ATOM    131  C   TRP    33      -7.314  -1.948   1.756  1.00  0.00
ATOM    132  O   TRP    33      -6.363  -1.672   1.120  1.00  0.00
ATOM    133  N   TRP    34      -7.478  -1.383   2.982  1.00  0.00
ATOM    134  CA  TRP    34      -6.844  -0.879   3.142  1.00  0.00
ATOM    135  C   TRP    34      -8.191  -1.031   3.818  1.00  0.00
ATOM    136  O   TRP    34      -8.361  -1.807   4.686  1.00  0.00
ATOM    137  N   LYS    35      -9.231  -0.253   3.412  1.00  0.00
ATOM    138  CA  LYS    35     -10.412  -0.359   3.977  1.00  0.00
ATOM    139  C   LYS    35      -9.816   0.405   2.813  1.00  0.00
ATOM    140  O   LYS    35      -9.993   0.067   1.699  1.00  0.00
ATOM    141  N   ALA    36      -9.057   1.507   3.058  1.00  0.00
ATOM    142  CA  ALA    36      -8.558   2.149   2.104  1.00  0.00
ATOM    143  C   ALA    36      -9.444   3.378   2.103  1.00  0.00
ATOM    144  O   ALA    36     -10.301   3.518   1.308  1.00  0.00
ATOM    145  N   LYS    37      -9.246   4.342   3.042  1.00  0.00
ATOM    146  CA  LYS    37      -9.963   5.342   3.046  1.00  0.00
ATOM    147  C   LYS    37      -8.552   5.210   2.511  1.00  0.00
ATOM    148  O   LYS    37      -8.286   5.496   1.401  1.00  0.00
ATOM    149  N   ALA    38      -7.569   4.752   3.331  1.00  0.00
ATOM    150  CA  ALA    38      -6.316   4.622   2.898  1.00  0.00
ATOM    151  C   ALA    38      -5.603   4.316   4.199  1.00  0.00
ATOM    152  O   ALA    38      -5.278   5.172   4.939  1.00  0.00
ATOM    153  N   ILE    39      -5.332   3.023   4.522  1.00  0.00
ATOM    154  CA  ILE    39      -4.757   2.773   5.571  1.00  0.00
ATOM    155  C   ILE    39      -4.872   3.120   7.041  1.00  0.00
ATOM    156  O   ILE    39      -4.270   4.015   7.511  1.00  0.00
ATOM    157  N   GLY    40      -5.692   2.382   7.837  1.00  0.00
ATOM    158  CA  GLY    40      -5.968   2.639   9.630  1.00  0.00
ATOM    159  C   GLY    40      -6.513   1.306  10.099  1.00  0.00
ATOM    160  O   GLY    40      -7.622   0.981   9.875  1.00  0.00
ATOM    161  N   SER    41      -5.704   0.463  10.794  1.00  0.00
ATOM    162  CA  SER    41      -6.150  -0.791  11.258  1.00  0.00
ATOM    163  C   SER    41      -6.064  -2.229  10.788  1.00  0.00
ATOM    164  O   SER    41      -6.907  -2.711  10.124  1.00  0.00
ATOM    165  N   GLY    42      -4.987  -2.981  11.142  1.00  0.00
ATOM    166  CA  GLY    42      -4.797  -4.460  10.718  1.00  0.00
ATOM    167  C   GLY    42      -4.728  -5.612   9.736  1.00  0.00
ATOM    168  O   GLY    42      -5.701  -6.143   9.342  1.00  0.00
ATOM    169  N   GLU    43      -3.514  -6.042   9.300  1.00  0.00
ATOM    170  CA  GLU    43      -3.307  -7.247   8.265  1.00  0.00
ATOM    171  C   GLU    43      -3.295  -6.628   6.883  1.00  0.00
ATOM    172  O   GLU    43      -4.250  -6.638   6.195  1.00  0.00
ATOM    173  N   ILE    44      -2.155  -6.045   6.424  1.00  0.00
ATOM    174  CA  ILE    44      -2.016  -5.361   4.991  1.00  0.00
ATOM    175  C   ILE    44      -0.996  -6.172   5.764  1.00  0.00
ATOM    176  O   ILE    44      -0.675  -7.249   5.416  1.00  0.00
ATOM    177  N   GLY    45      -0.438  -5.643   6.886  1.00  0.00
ATOM    178  CA  GLY    45       0.250  -6.242   7.370  1.00  0.00
ATOM    179  C   GLY    45       0.735  -4.931   6.786  1.00  0.00
ATOM    180  O   GLY    45       0.487  -3.900   7.297  1.00  0.00
ATOM    181  N   TYR    46       1.474  -4.944   5.644  1.00  0.00
ATOM    182  CA  TYR    46       1.975  -3.730   5.022  1.00  0.00
ATOM    183  C   TYR    46       2.699  -2.418   4.802  1.00  0.00
ATOM    184  O   TYR    46       2.258  -1.398   5.192  1.00  0.00
ATOM    185  N   ILE    47       3.887  -2.416   4.139  1.00  0.00
ATOM    186  CA  ILE    47       4.566  -1.271   3.921  1.00  0.00
ATOM    187  C   ILE    47       5.645  -0.565   4.716  1.00  0.00
ATOM    188  O   ILE    47       5.387   0.303   5.468  1.00  0.00
ATOM    189  N   PRO    48       6.942  -0.942   4.559  1.00  0.00
ATOM    190  CA  PRO    48       8.243  -0.257   5.367  1.00  0.00
ATOM    191  C   PRO    48       7.832   1.064   4.750  1.00  0.00
ATOM    192  O   PRO    48       7.301   1.901   5.385  1.00  0.00
ATOM    193  N   ALA    49       8.081   1.290   3.432  1.00  0.00
ATOM    194  CA  ALA    49       7.772   2.242   3.037  1.00  0.00
ATOM    195  C   ALA    49       7.290   3.626   2.655  1.00  0.00
ATOM    196  O   ALA    49       6.208   3.999   2.930  1.00  0.00
ATOM    197  N   ASN    50       8.126   4.459   1.978  1.00  0.00
ATOM    198  CA  ASN    50       7.744   5.197   1.824  1.00  0.00
ATOM    199  C   ASN    50       6.502   4.336   1.925  1.00  0.00
ATOM    200  O   ASN    50       5.694   4.516   2.761  1.00  0.00
ATOM    201  N   TYR    51       6.315   3.330   1.028  1.00  0.00
ATOM    202  CA  TYR    51       5.178   2.490   1.066  1.00  0.00
ATOM    203  C   TYR    51       3.828   1.805   1.119  1.00  0.00
ATOM    204  O   TYR    51       3.173   1.812   2.097  1.00  0.00
ATOM    205  N   ILE    52       3.360   1.168   0.013  1.00  0.00
ATOM    206  CA  ILE    52       2.090   0.497  -0.011  1.00  0.00
ATOM    207  C   ILE    52       1.366  -0.688  -0.617  1.00  0.00
ATOM    208  O   ILE    52       1.745  -1.201  -1.606  1.00  0.00
ATOM    209  N   ALA    53       0.253  -1.172  -0.004  1.00  0.00
ATOM    210  CA  ALA    53      -0.366  -2.163  -0.496  1.00  0.00
ATOM    211  C   ALA    53      -1.030  -3.408  -1.048  1.00  0.00
ATOM    212  O   ALA    53      -0.649  -3.921  -2.036  1.00  0.00
ATOM    213  N   ALA    54      -2.091  -3.945  -0.388  1.00  0.00
ATOM    214  CA  ALA    54      -2.788  -5.145  -0.855  1.00  0.00
ATOM    215  C   ALA    54      -3.783  -6.005  -1.607  1.00  0.00
ATOM    216  O   ALA    54      -4.654  -5.528  -2.239  1.00  0.00
ATOM    217  N   ALA    55      -3.668  -7.359  -1.553  1.00  0.00
ATOM    218  CA  ALA    55      -4.614  -8.307  -2.272  1.00  0.00
ATOM    219  C   ALA    55      -5.238  -9.123  -3.386  1.00  0.00
ATOM    220  O   ALA    55      -5.981  -8.639  -4.161  1.00  0.00
ATOM    221  N   GLU    56      -4.935 -10.444  -3.493  1.00  0.00
ATOM    222  CA  GLU    56      -5.468 -11.210  -4.470  1.00  0.00
ATOM    223  C   GLU    56      -5.837 -12.659  -4.714  1.00  0.00
ATOM    224  O   GLU    56      -5.268 -13.538  -4.177  1.00  0.00
ATOM    225  OXT GLU    56      -5.168 -14.702  -4.030  1.00  0.00
TER   
END




