REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0079AL009_5 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0079  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0079, MarA   
REMARK  
METHOD This prediction is based, in part, on a threading algorithm described in  
METHOD three publications:  
METHOD (i) "An Efficient Computational Method for Globally Optimal Threading",  
METHOD by Y. Xu, D. Xu, and E.C. Uberbacher, Journal of Computational Biology,   
METHOD Vol. 5(3), pp. 609-626, 1998.  
METHOD (ii) "A New Method for Modeling and Solving the Protein Fold Recognition  
METHOD Problem", by Y. Xu, D. Xu, and E.C. Uberbacher, Proc. of RECOMB 98  
METHOD Second Annual Int'l Conf. on Computational Molecular Biology  
METHOD March 22-25, 1998, NEW York, NY, ACM Press, pp. 285-292.  
METHOD (iii) "A polynomial-time algorithm for a class of protein threading  
METHOD problems", by Ying Xu and Edward C. Uberbacher, CABIOS, Vol. 12 (6),  
METHOD pp.511-517, 1996.  
METHOD  
METHOD  
METHOD The prediction is also based, in part, on a different threading algorithm  
METHOD described in the following publication:  
METHOD (iv) "A fast, reliable method for threading", by O.H. Crawford, submitted  
METHOD to Bioinformatics (journal)  
METHOD  
METHOD  
METHOD The energy model employed in the threading is based on improvements and  
METHOD extensions of the energy modeling described in Refs. (ii) and (iii)  
METHOD and in the following paper:  
METHOD (v) "Protein Fold Recognition at the Secondary Structure Level",  
METHOD by D. Xu, M.A. Unseren, Y. Xu, and E.C. Uberbacher, Submitted.  
METHOD  
METHOD  
METHOD  
METHOD Members of Oak Ridge National Laboratory's Computational Biosciences  
METHOD Section participating in CASP3  include (in alphabetical order):  
METHOD Oakley Crawford, J. Ralph Einstein, Frank W. Larimer, Richard Mural,  
METHOD Edward C. Uberbacher, Michael A. Unseren, Dong Xu, Ying Xu, and Ge Zhang  
MODEL  5   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2aac_A 
ATOM      1  N   ILE    13      14.213  22.648  46.669  1.00  0.00              
ATOM      2  CA  ILE    13      14.175  21.311  47.220  1.00  0.00              
ATOM      3  C   ILE    13      14.295  21.600  48.712  1.00  0.00              
ATOM      4  O   ILE    13      14.895  22.612  49.123  1.00  0.00              
ATOM      5  N   HIS    14      13.695  20.741  49.523  1.00  0.00              
ATOM      6  CA  HIS    14      13.675  20.935  50.964  1.00  0.00              
ATOM      7  C   HIS    14      15.004  21.250  51.609  1.00  0.00              
ATOM      8  O   HIS    14      15.100  22.146  52.443  1.00  0.00              
ATOM      9  N   SER    15      16.047  20.551  51.186  1.00  0.00              
ATOM     10  CA  SER    15      17.371  20.725  51.775  1.00  0.00              
ATOM     11  C   SER    15      18.154  21.953  51.334  1.00  0.00              
ATOM     12  O   SER    15      19.262  22.190  51.798  1.00  0.00              
ATOM     13  N   ILE    16      17.562  22.744  50.456  1.00  0.00              
ATOM     14  CA  ILE    16      18.203  23.966  50.001  1.00  0.00              
ATOM     15  C   ILE    16      18.029  25.101  51.008  1.00  0.00              
ATOM     16  O   ILE    16      18.679  26.134  50.880  1.00  0.00              
ATOM     17  N   LEU    17      17.121  24.927  51.965  1.00  0.00              
ATOM     18  CA  LEU    17      16.810  25.966  52.962  1.00  0.00              
ATOM     19  C   LEU    17      17.993  26.712  53.559  1.00  0.00              
ATOM     20  O   LEU    17      17.990  27.948  53.603  1.00  0.00              
ATOM     21  N   ASP    18      19.011  25.973  53.988  1.00  0.00              
ATOM     22  CA  ASP    18      20.201  26.568  54.596  1.00  0.00              
ATOM     23  C   ASP    18      21.087  27.334  53.609  1.00  0.00              
ATOM     24  O   ASP    18      22.041  27.999  54.003  1.00  0.00              
ATOM     25  N   TRP    19      20.781  27.221  52.325  1.00  0.00              
ATOM     26  CA  TRP    19      21.552  27.891  51.293  1.00  0.00              
ATOM     27  C   TRP    19      20.747  29.063  50.723  1.00  0.00              
ATOM     28  O   TRP    19      21.163  29.713  49.764  1.00  0.00              
ATOM     29  N   ILE    20      19.589  29.319  51.306  1.00  0.00              
ATOM     30  CA  ILE    20      18.749  30.398  50.820  1.00  0.00              
ATOM     31  C   ILE    20      18.592  31.507  51.845  1.00  0.00              
ATOM     32  O   ILE    20      17.697  32.337  51.725  1.00  0.00              
ATOM     33  N   LYS    41      32.762  35.910  39.587  1.00  0.00              
ATOM     34  CA  LYS    41      31.788  36.509  38.677  1.00  0.00              
ATOM     35  C   LYS    41      31.515  35.723  37.389  1.00  0.00              
ATOM     36  O   LYS    41      30.374  35.316  37.132  1.00  0.00              
ATOM     37  N   TRP    42      32.563  35.434  36.592  1.00  0.00              
ATOM     38  CA  TRP    42      32.342  34.686  35.349  1.00  0.00              
ATOM     39  C   TRP    42      31.691  33.330  35.540  1.00  0.00              
ATOM     40  O   TRP    42      30.864  32.904  34.725  1.00  0.00              
ATOM     41  N   HIS    43      32.027  32.659  36.626  1.00  0.00              
ATOM     42  CA  HIS    43      31.454  31.344  36.868  1.00  0.00              
ATOM     43  C   HIS    43      29.983  31.435  37.189  1.00  0.00              
ATOM     44  O   HIS    43      29.188  30.627  36.708  1.00  0.00              
ATOM     45  N   LEU    44      29.610  32.430  37.982  1.00  0.00              
ATOM     46  CA  LEU    44      28.209  32.604  38.324  1.00  0.00              
ATOM     47  C   LEU    44      27.430  33.079  37.112  1.00  0.00              
ATOM     48  O   LEU    44      26.287  32.703  36.910  1.00  0.00              
ATOM     49  N   GLN    45      28.066  33.914  36.303  1.00  0.00              
ATOM     50  CA  GLN    45      27.466  34.438  35.095  1.00  0.00              
ATOM     51  C   GLN    45      27.173  33.267  34.165  1.00  0.00              
ATOM     52  O   GLN    45      26.061  33.134  33.648  1.00  0.00              
ATOM     53  N   ARG    46      28.166  32.404  33.971  1.00  0.00              
ATOM     54  CA  ARG    46      27.984  31.256  33.096  1.00  0.00              
ATOM     55  C   ARG    46      26.931  30.299  33.625  1.00  0.00              
ATOM     56  O   ARG    46      26.092  29.811  32.874  1.00  0.00              
ATOM     57  N   MET    47      26.986  30.035  34.928  1.00  0.00              
ATOM     58  CA  MET    47      26.059  29.110  35.555  1.00  0.00              
ATOM     59  C   MET    47      24.633  29.635  35.460  1.00  0.00              
ATOM     60  O   MET    47      23.692  28.896  35.126  1.00  0.00              
ATOM     61  N   PHE    48      24.481  30.937  35.691  1.00  0.00              
ATOM     62  CA  PHE    48      23.169  31.539  35.594  1.00  0.00              
ATOM     63  C   PHE    48      22.640  31.369  34.173  1.00  0.00              
ATOM     64  O   PHE    48      21.474  31.016  33.979  1.00  0.00              
ATOM     65  N   LYS    49      23.508  31.569  33.181  1.00  0.00              
ATOM     66  CA  LYS    49      23.129  31.387  31.794  1.00  0.00              
ATOM     67  C   LYS    49      22.692  29.954  31.517  1.00  0.00              
ATOM     68  O   LYS    49      21.727  29.732  30.771  1.00  0.00              
ATOM     69  N   LYS    50      23.364  28.981  32.144  1.00  0.00              
ATOM     70  CA  LYS    50      23.032  27.549  31.985  1.00  0.00              
ATOM     71  C   LYS    50      21.667  27.272  32.569  1.00  0.00              
ATOM     72  O   LYS    50      20.919  26.446  32.042  1.00  0.00              
ATOM     73  N   GLU    51      21.383  27.900  33.712  1.00  0.00              
ATOM     74  CA  GLU    51      20.083  27.744  34.345  1.00  0.00              
ATOM     75  C   GLU    51      19.000  28.191  33.373  1.00  0.00              
ATOM     76  O   GLU    51      18.042  27.467  33.126  1.00  0.00              
ATOM     77  N   THR    52      19.184  29.364  32.773  1.00  0.00              
ATOM     78  CA  THR    52      18.196  29.881  31.827  1.00  0.00              
ATOM     79  C   THR    52      18.052  28.923  30.638  1.00  0.00              
ATOM     80  O   THR    52      16.945  28.532  30.258  1.00  0.00              
ATOM     81  N   GLY    53      19.189  28.543  30.066  1.00  0.00              
ATOM     82  CA  GLY    53      19.212  27.626  28.939  1.00  0.00              
ATOM     83  C   GLY    53      18.427  26.341  29.253  1.00  0.00              
ATOM     84  O   GLY    53      17.539  25.943  28.490  1.00  0.00              
ATOM     85  N   HIS    54      18.708  25.736  30.408  1.00  0.00              
ATOM     86  CA  HIS    54      18.027  24.510  30.816  1.00  0.00              
ATOM     87  C   HIS    54      16.550  24.768  31.062  1.00  0.00              
ATOM     88  O   HIS    54      15.678  24.028  30.589  1.00  0.00              
ATOM     89  N   SER    55      16.290  25.816  31.840  1.00  0.00              
ATOM     90  CA  SER    55      14.942  26.185  32.211  1.00  0.00              
ATOM     91  C   SER    55      14.049  26.465  31.032  1.00  0.00              
ATOM     92  O   SER    55      12.846  26.226  31.105  1.00  0.00              
ATOM     93  N   ILE    60      14.308  19.218  31.215  1.00  0.00              
ATOM     94  CA  ILE    60      14.720  20.622  31.230  1.00  0.00              
ATOM     95  C   ILE    60      14.557  21.271  32.604  1.00  0.00              
ATOM     96  O   ILE    60      15.485  21.893  33.130  1.00  0.00              
ATOM     97  N   ARG    61      13.403  21.071  33.218  1.00  0.00              
ATOM     98  CA  ARG    61      13.143  21.642  34.517  1.00  0.00              
ATOM     99  C   ARG    61      14.046  21.054  35.582  1.00  0.00              
ATOM    100  O   ARG    61      14.600  21.780  36.391  1.00  0.00              
ATOM    101  N   SER    62      14.219  19.735  35.552  1.00  0.00              
ATOM    102  CA  SER    62      15.062  19.056  36.527  1.00  0.00              
ATOM    103  C   SER    62      16.489  19.562  36.392  1.00  0.00              
ATOM    104  O   SER    62      17.184  19.785  37.388  1.00  0.00              
ATOM    105  N   ARG    63      16.926  19.710  35.147  1.00  0.00              
ATOM    106  CA  ARG    63      18.268  20.200  34.861  1.00  0.00              
ATOM    107  C   ARG    63      18.403  21.654  35.380  1.00  0.00              
ATOM    108  O   ARG    63      19.409  22.002  36.001  1.00  0.00              
ATOM    109  N   LYS    64      17.387  22.485  35.171  1.00  0.00              
ATOM    110  CA  LYS    64      17.435  23.868  35.674  1.00  0.00              
ATOM    111  C   LYS    64      17.506  23.866  37.203  1.00  0.00              
ATOM    112  O   LYS    64      18.266  24.618  37.801  1.00  0.00              
ATOM    113  N   MET    65      16.694  23.027  37.838  1.00  0.00              
ATOM    114  CA  MET    65      16.685  22.914  39.286  1.00  0.00              
ATOM    115  C   MET    65      18.070  22.504  39.766  1.00  0.00              
ATOM    116  O   MET    65      18.606  23.066  40.725  1.00  0.00              
ATOM    117  N   THR    66      18.643  21.510  39.080  1.00  0.00              
ATOM    118  CA  THR    66      19.958  21.014  39.411  1.00  0.00              
ATOM    119  C   THR    66      21.000  22.123  39.321  1.00  0.00              
ATOM    120  O   THR    66      21.827  22.287  40.214  1.00  0.00              
ATOM    121  N   GLU    67      20.955  22.878  38.222  1.00  0.00              
ATOM    122  CA  GLU    67      21.901  23.963  37.996  1.00  0.00              
ATOM    123  C   GLU    67      21.722  25.071  39.049  1.00  0.00              
ATOM    124  O   GLU    67      22.691  25.697  39.491  1.00  0.00              
ATOM    125  N   ILE    68      20.472  25.308  39.442  1.00  0.00              
ATOM    126  CA  ILE    68      20.161  26.283  40.474  1.00  0.00              
ATOM    127  C   ILE    68      20.788  25.813  41.789  1.00  0.00              
ATOM    128  O   ILE    68      21.401  26.588  42.525  1.00  0.00              
ATOM    129  N   ALA    69      20.606  24.533  42.105  1.00  0.00              
ATOM    130  CA  ALA    69      21.202  23.961  43.305  1.00  0.00              
ATOM    131  C   ALA    69      22.715  24.208  43.258  1.00  0.00              
ATOM    132  O   ALA    69      23.338  24.536  44.273  1.00  0.00              
ATOM    133  N   GLN    70      23.310  23.999  42.087  1.00  0.00              
ATOM    134  CA  GLN    70      24.726  24.220  41.939  1.00  0.00              
ATOM    135  C   GLN    70      25.061  25.668  42.279  1.00  0.00              
ATOM    136  O   GLN    70      26.004  25.930  43.015  1.00  0.00              
ATOM    137  N   LYS    71      24.278  26.611  41.754  1.00  0.00              
ATOM    138  CA  LYS    71      24.538  28.017  42.036  1.00  0.00              
ATOM    139  C   LYS    71      24.477  28.278  43.538  1.00  0.00              
ATOM    140  O   LYS    71      25.361  28.908  44.092  1.00  0.00              
ATOM    141  N   LEU    72      23.451  27.759  44.204  1.00  0.00              
ATOM    142  CA  LEU    72      23.316  27.935  45.643  1.00  0.00              
ATOM    143  C   LEU    72      24.530  27.368  46.374  1.00  0.00              
ATOM    144  O   LEU    72      25.063  27.982  47.296  1.00  0.00              
ATOM    145  N   LYS    73      24.970  26.185  45.961  1.00  0.00              
ATOM    146  CA  LYS    73      26.122  25.551  46.575  1.00  0.00              
ATOM    147  C   LYS    73      27.414  26.289  46.254  1.00  0.00              
ATOM    148  O   LYS    73      28.278  26.413  47.134  1.00  0.00              
ATOM    149  N   GLU    74      27.528  26.813  45.033  1.00  0.00              
ATOM    150  CA  GLU    74      28.719  27.578  44.624  1.00  0.00              
ATOM    151  C   GLU    74      28.769  28.854  45.480  1.00  0.00              
ATOM    152  O   GLU    74      29.859  29.334  45.805  1.00  0.00              
ATOM    153  N   SER    75      27.605  29.386  45.841  1.00  0.00              
ATOM    154  CA  SER    75      27.567  30.572  46.695  1.00  0.00              
ATOM    155  C   SER    75      28.005  30.183  48.111  1.00  0.00              
ATOM    156  O   SER    75      28.845  30.859  48.713  1.00  0.00              
ATOM    157  N   ASN    76      27.494  29.069  48.615  1.00  0.00              
ATOM    158  CA  ASN    76      27.843  28.600  49.957  1.00  0.00              
ATOM    159  C   ASN    76      29.334  28.373  50.002  1.00  0.00              
ATOM    160  O   ASN    76      29.999  28.765  50.944  1.00  0.00              
ATOM    161  N   GLU    77      29.853  27.758  48.950  1.00  0.00              
ATOM    162  CA  GLU    77      31.273  27.492  48.843  1.00  0.00              
ATOM    163  C   GLU    77      32.065  28.807  48.794  1.00  0.00              
ATOM    164  O   GLU    77      33.062  28.965  49.480  1.00  0.00              
ATOM    165  N   PRO    78      31.596  29.755  47.988  1.00  0.00              
ATOM    166  CA  PRO    78      32.285  31.030  47.837  1.00  0.00              
ATOM    167  C   PRO    78      32.345  31.850  49.116  1.00  0.00              
ATOM    168  O   PRO    78      33.394  32.413  49.432  1.00  0.00              
ATOM    169  N   ILE    79      31.249  31.898  49.869  1.00  0.00              
ATOM    170  CA  ILE    79      31.260  32.685  51.099  1.00  0.00              
ATOM    171  C   ILE    79      31.875  31.951  52.293  1.00  0.00              
ATOM    172  O   ILE    79      32.163  32.567  53.322  1.00  0.00              
END
