
PFRMAT TS
TARGET T0102
AUTHOR 5477-6509-1337
REMARK
REMARK   Work performed by Kai-Ming Ho, James R. Morris, Cai-Zhuang Wang,
REMARK                   Drena Dobbs, Tzu-Liang Chan, Young-Ok Im,
REMARK                   Josh Koch, Neil Voss, Dion Harmon
REMARK
REMARK   Acknowledgments to Amy Andreotti and Josh Lapan
REMARK
REMARK   Work supported by Pioneer Hi-Bred, by a Carver Foundation grant
REMARK     from Iowa State University, and a Laboratory Directed 
REMARK     Research and Development grant from Ames Laboratory, U.S.D.O.E.
REMARK
REMARK
METHOD
METHOD   This structure is an ab initio prediction, produced by a
METHOD   genetic algorithm approach performed on parallel machines, to
METHOD   optimize our coarse grained molecular dynamics model (two beads,
METHOD   one for the backbone and one for the side chain) for this
METHOD   sequence. Four different models were generated with this
METHOD   approach, using different initial conditions and
METHOD   simulation schedules.  These models either did not enforce the
METHOD   cyclic structure for this system, or did so with weak
METHOD   constraints.  All of these produced similar geometries.
METHOD   Model 2 was the lowest energy ab initio structure that we
METHOD   produced. It is very similar in topology to model 1 (produced
METHOD   by structure recognition), although the RMSD between the
METHOD   C-alpha atoms in the two models is fairly large (8.3 angstroms).
METHOD
METHOD   All atom models were generated using the MaxSprout Server (L. Holm,
METHOD   C. Sander (1991) J. Mol. Biol. 218:183-194), using the CA positions
METHOD   from the coarse grained model. The all-atom version does
METHOD   not preserve the CA positions, and the resultant backbone is
METHOD   "broken," lacking appropriate covalent bonds.  Therefore the
METHOD   original CA trace has also been submitted as an unrefined model.
METHOD
MODEL 2 unrefined
PARENT N/A
ATOM      1  CA  MET     1       4.164   9.788  -1.745  1.00  5.00           C
ATOM      2  CA  ALA     2       5.475  10.707   1.753  1.00  5.00           C
ATOM      3  CA  LYS     3       7.917   7.755   1.490  1.00  5.00           C
ATOM      4  CA  GLU     4       5.786   5.960   4.096  1.00  5.00           C
ATOM      5  CA  PHE     5       4.369   3.996   1.148  1.00  5.00           C
ATOM      6  CA  GLY     6       8.004   3.181   0.325  1.00  5.00           C
ATOM      7  CA  ILE     7       8.302   1.894   3.904  1.00  5.00           C
ATOM      8  CA  PRO     8      11.796   0.674   3.061  1.00  5.00           C
ATOM      9  CA  ALA     9      12.071  -1.631   0.059  1.00  5.00           C
ATOM     10  CA  ALA    10      14.143  -4.047   2.128  1.00  5.00           C
ATOM     11  CA  VAL    11      11.447  -3.856   4.821  1.00  5.00           C
ATOM     12  CA  ALA    12       8.414  -5.972   3.883  1.00  5.00           C
ATOM     13  CA  GLY    13       9.765  -5.707   0.325  1.00  5.00           C
ATOM     14  CA  THR    14       7.154  -8.292  -0.702  1.00  5.00           C
ATOM     15  CA  VAL    15       4.594  -6.057   1.031  1.00  5.00           C
ATOM     16  CA  LEU    16       5.975  -3.254  -1.158  1.00  5.00           C
ATOM     17  CA  ASN    17       5.100  -5.509  -4.108  1.00  5.00           C
ATOM     18  CA  VAL    18       1.548  -5.516  -2.716  1.00  5.00           C
ATOM     19  CA  VAL    19      -0.057  -8.946  -3.178  1.00  5.00           C
ATOM     20  CA  GLU    20       2.896  -9.826  -5.435  1.00  5.00           C
ATOM     21  CA  ALA    21       0.982  -8.529  -8.469  1.00  5.00           C
ATOM     22  CA  GLY    22      -2.219 -10.230  -7.280  1.00  5.00           C
ATOM     23  CA  GLY    23      -4.422  -7.640  -9.019  1.00  5.00           C
ATOM     24  CA  TRP    24      -2.006  -4.829  -8.123  1.00  5.00           C
ATOM     25  CA  VAL    25      -2.017  -2.688  -4.966  1.00  5.00           C
ATOM     26  CA  THR    26      -5.287  -0.858  -4.251  1.00  5.00           C
ATOM     27  CA  THR    27      -7.194  -1.100  -0.956  1.00  5.00           C
ATOM     28  CA  ILE    28      -3.841  -1.567   0.802  1.00  5.00           C
ATOM     29  CA  VAL    29      -4.308  -5.301   0.176  1.00  5.00           C
ATOM     30  CA  SER    30      -7.407  -5.021   2.384  1.00  5.00           C
ATOM     31  CA  ILE    31      -5.116  -3.478   5.015  1.00  5.00           C
ATOM     32  CA  LEU    32      -2.822  -6.479   4.477  1.00  5.00           C
ATOM     33  CA  THR    33      -5.854  -8.687   5.172  1.00  5.00           C
ATOM     34  CA  ALA    34      -4.016 -11.500   3.366  1.00  5.00           C
ATOM     35  CA  VAL    35      -1.107 -10.852   5.747  1.00  5.00           C
ATOM     36  CA  GLY    36      -3.615 -11.226   8.597  1.00  5.00           C
ATOM     37  CA  SER    37      -1.180  -9.469  10.961  1.00  5.00           C
ATOM     38  CA  GLY    38       1.567 -11.816   9.737  1.00  5.00           C
ATOM     39  CA  GLY    39       4.167  -9.292  10.932  1.00  5.00           C
ATOM     40  CA  LEU    40       2.214  -6.511   9.162  1.00  5.00           C
ATOM     41  CA  SER    41       3.021  -4.173  12.084  1.00  5.00           C
ATOM     42  CA  LEU    42       4.867  -1.918   9.623  1.00  5.00           C
ATOM     43  CA  LEU    43       1.753  -2.089   7.425  1.00  5.00           C
ATOM     44  CA  ALA    44      -0.126  -0.881  10.517  1.00  5.00           C
ATOM     45  CA  ALA    45       2.314   2.050  10.431  1.00  5.00           C
ATOM     46  CA  ALA    46       1.198   2.516   6.813  1.00  5.00           C
ATOM     47  CA  GLY    47      -2.352   2.725   8.195  1.00  5.00           C
ATOM     48  CA  ARG    48      -2.076   6.526   8.029  1.00  5.00           C
ATOM     49  CA  GLU    49      -5.858   6.649   7.401  1.00  5.00           C
ATOM     50  CA  SER    50      -5.348   4.057   4.648  1.00  5.00           C
ATOM     51  CA  ILE    51      -2.763   6.430   3.152  1.00  5.00           C
ATOM     52  CA  LYS    52      -5.516   9.070   3.201  1.00  5.00           C
ATOM     53  CA  ALA    53      -7.583   6.595   1.163  1.00  5.00           C
ATOM     54  CA  TYR    54      -4.613   6.479  -1.228  1.00  5.00           C
ATOM     55  CA  LEU    55      -4.847  10.285  -1.338  1.00  5.00           C
ATOM     56  CA  LYS    56      -8.441   9.700  -2.476  1.00  5.00           C
ATOM     57  CA  LYS    57      -6.876   7.540  -5.204  1.00  5.00           C
ATOM     58  CA  GLU    58      -4.836  10.663  -6.006  1.00  5.00           C
ATOM     59  CA  ILE    59      -8.221  12.240  -6.786  1.00  5.00           C
ATOM     60  CA  LYS    60      -8.707   9.381  -9.265  1.00  5.00           C
ATOM     61  CA  LYS    61      -5.290  10.316 -10.681  1.00  5.00           C
ATOM     62  CA  LYS    62      -6.474   8.997 -14.067  1.00  5.00           C
ATOM     63  CA  GLY    63      -7.505   5.798 -12.261  1.00  5.00           C
ATOM     64  CA  LYS    64      -4.720   3.583 -10.886  1.00  5.00           C
ATOM     65  CA  ARG    65      -2.473   6.568 -11.659  1.00  5.00           C
ATOM     66  CA  ALA    66       0.311   3.977 -11.957  1.00  5.00           C
ATOM     67  CA  VAL    67      -0.764   2.842  -8.477  1.00  5.00           C
ATOM     68  CA  ILE    68      -0.305   6.483  -7.435  1.00  5.00           C
ATOM     69  CA  ALA    69       3.236   6.193  -8.825  1.00  5.00           C
ATOM     70  CA  TRP    70       3.635   3.145  -6.565  1.00  5.00           C
TER
END


