REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0085AL009_3_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0085  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0085, Cytochrome c554   
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1fgj_A 
ATOM      1  N   ARG     8       9.749  27.228  35.696  1.00  0.00              
ATOM      2  CA  ARG     8      11.167  26.936  35.500  1.00  0.00              
ATOM      3  C   ARG     8      12.043  28.139  35.082  1.00  0.00              
ATOM      4  O   ARG     8      13.060  28.431  35.724  1.00  0.00              
ATOM      5  N   LYS     9      11.627  28.835  34.024  1.00  0.00              
ATOM      6  CA  LYS     9      12.345  29.991  33.487  1.00  0.00              
ATOM      7  C   LYS     9      12.251  31.247  34.344  1.00  0.00              
ATOM      8  O   LYS     9      13.084  32.142  34.222  1.00  0.00              
ATOM      9  N   LYS    10      11.201  31.337  35.159  1.00  0.00              
ATOM     10  CA  LYS    10      10.990  32.486  36.058  1.00  0.00              
ATOM     11  C   LYS    10      12.013  32.468  37.182  1.00  0.00              
ATOM     12  O   LYS    10      12.527  33.516  37.585  1.00  0.00              
ATOM     13  N   CYS    11      12.256  31.272  37.717  1.00  0.00              
ATOM     14  CA  CYS    11      13.200  31.081  38.814  1.00  0.00              
ATOM     15  C   CYS    11      14.532  31.708  38.448  1.00  0.00              
ATOM     16  O   CYS    11      15.065  32.546  39.170  1.00  0.00              
ATOM     17  N   SER    12      15.002  31.371  37.257  1.00  0.00              
ATOM     18  CA  SER    12      16.263  31.875  36.760  1.00  0.00              
ATOM     19  C   SER    12      16.232  33.377  36.502  1.00  0.00              
ATOM     20  O   SER    12      17.072  34.109  37.022  1.00  0.00              
ATOM     21  N   SER    13      15.245  33.845  35.739  1.00  0.00              
ATOM     22  CA  SER    13      15.167  35.268  35.418  1.00  0.00              
ATOM     23  C   SER    13      15.140  36.179  36.633  1.00  0.00              
ATOM     24  O   SER    13      15.983  37.077  36.756  1.00  0.00              
ATOM     25  N   CYS    14      14.175  35.955  37.523  1.00  0.00              
ATOM     26  CA  CYS    14      14.051  36.776  38.717  1.00  0.00              
ATOM     27  C   CYS    14      15.309  36.707  39.553  1.00  0.00              
ATOM     28  O   CYS    14      15.822  37.730  40.014  1.00  0.00              
ATOM     29  N   HIS    15      15.820  35.502  39.745  1.00  0.00              
ATOM     30  CA  HIS    15      17.020  35.348  40.540  1.00  0.00              
ATOM     31  C   HIS    15      18.286  35.906  39.924  1.00  0.00              
ATOM     32  O   HIS    15      19.260  36.128  40.635  1.00  0.00              
ATOM     33  N   LYS    16      18.259  36.195  38.624  1.00  0.00              
ATOM     34  CA  LYS    16      19.420  36.783  37.956  1.00  0.00              
ATOM     35  C   LYS    16      19.716  38.111  38.630  1.00  0.00              
ATOM     36  O   LYS    16      20.870  38.533  38.733  1.00  0.00              
ATOM     37  N   ALA    17      18.652  38.761  39.089  1.00  0.00              
ATOM     38  CA  ALA    17      18.762  40.035  39.771  1.00  0.00              
ATOM     39  C   ALA    17      18.774  39.816  41.269  1.00  0.00              
ATOM     40  O   ALA    17      19.604  40.394  41.964  1.00  0.00              
ATOM     41  N   GLN    18      17.879  38.959  41.760  1.00  0.00              
ATOM     42  CA  GLN    18      17.782  38.689  43.194  1.00  0.00              
ATOM     43  C   GLN    18      18.986  38.019  43.836  1.00  0.00              
ATOM     44  O   GLN    18      19.412  38.413  44.919  1.00  0.00              
ATOM     45  N   GLN    20      22.244  37.073  42.015  1.00  0.00              
ATOM     46  CA  GLN    20      23.185  37.115  40.892  1.00  0.00              
ATOM     47  C   GLN    20      24.176  35.957  40.814  1.00  0.00              
ATOM     48  O   GLN    20      24.140  35.166  39.867  1.00  0.00              
ATOM     49  N   SER    21      25.038  35.851  41.821  1.00  0.00              
ATOM     50  CA  SER    21      26.065  34.815  41.868  1.00  0.00              
ATOM     51  C   SER    21      25.493  33.393  41.908  1.00  0.00              
ATOM     52  O   SER    21      26.107  32.463  41.383  1.00  0.00              
ATOM     53  N   TRP    22      24.296  33.231  42.473  1.00  0.00              
ATOM     54  CA  TRP    22      23.653  31.913  42.550  1.00  0.00              
ATOM     55  C   TRP    22      23.228  31.372  41.184  1.00  0.00              
ATOM     56  O   TRP    22      23.270  30.162  40.946  1.00  0.00              
ATOM     57  N   LYS    23      22.806  32.275  40.302  1.00  0.00              
ATOM     58  CA  LYS    23      22.381  31.917  38.953  1.00  0.00              
ATOM     59  C   LYS    23      23.592  31.641  38.053  1.00  0.00              
ATOM     60  O   LYS    23      23.603  30.673  37.297  1.00  0.00              
ATOM     61  N   ASP    24      24.608  32.489  38.152  1.00  0.00              
ATOM     62  CA  ASP    24      25.824  32.333  37.370  1.00  0.00              
ATOM     63  C   ASP    24      26.525  31.017  37.692  1.00  0.00              
ATOM     64  O   ASP    24      26.840  30.239  36.795  1.00  0.00              
ATOM     65  N   THR    25      26.767  30.776  38.978  1.00  0.00              
ATOM     66  CA  THR    25      27.427  29.550  39.436  1.00  0.00              
ATOM     67  C   THR    25      26.714  28.284  38.943  1.00  0.00              
ATOM     68  O   THR    25      27.358  27.292  38.606  1.00  0.00              
ATOM     69  N   ALA    26      25.386  28.322  38.925  1.00  0.00              
ATOM     70  CA  ALA    26      24.595  27.196  38.462  1.00  0.00              
ATOM     71  C   ALA    26      24.729  27.030  36.946  1.00  0.00              
ATOM     72  O   ALA    26      24.953  25.927  36.460  1.00  0.00              
ATOM     73  N   HIS    27      24.575  28.123  36.204  1.00  0.00              
ATOM     74  CA  HIS    27      24.686  28.085  34.750  1.00  0.00              
ATOM     75  C   HIS    27      26.020  27.511  34.297  1.00  0.00              
ATOM     76  O   HIS    27      26.083  26.746  33.346  1.00  0.00              
ATOM     77  N   MET    31      23.916  19.603  30.802  1.00  0.00              
ATOM     78  CA  MET    31      23.826  18.169  30.571  1.00  0.00              
ATOM     79  C   MET    31      24.249  17.693  29.179  1.00  0.00              
ATOM     80  O   MET    31      24.784  16.592  29.044  1.00  0.00              
ATOM     81  N   GLU    32      24.053  18.527  28.157  1.00  0.00              
ATOM     82  CA  GLU    32      24.420  18.167  26.775  1.00  0.00              
ATOM     83  C   GLU    32      25.892  17.789  26.630  1.00  0.00              
ATOM     84  O   GLU    32      26.224  16.803  25.979  1.00  0.00              
ATOM     85  N   SER    33      26.765  18.565  27.257  1.00  0.00              
ATOM     86  CA  SER    33      28.193  18.296  27.223  1.00  0.00              
ATOM     87  C   SER    33      28.468  16.845  27.648  1.00  0.00              
ATOM     88  O   SER    33      29.151  16.092  26.945  1.00  0.00              
ATOM     89  N   LEU    34      27.877  16.443  28.769  1.00  0.00              
ATOM     90  CA  LEU    34      28.063  15.094  29.294  1.00  0.00              
ATOM     91  C   LEU    34      27.708  14.027  28.252  1.00  0.00              
ATOM     92  O   LEU    34      28.373  12.999  28.166  1.00  0.00              
ATOM     93  N   LYS    35      26.697  14.303  27.433  1.00  0.00              
ATOM     94  CA  LYS    35      26.246  13.371  26.402  1.00  0.00              
ATOM     95  C   LYS    35      27.163  13.280  25.200  1.00  0.00              
ATOM     96  O   LYS    35      27.367  12.201  24.642  1.00  0.00              
ATOM     97  N   VAL    38      21.263   7.763  36.167  1.00  0.00              
ATOM     98  CA  VAL    38      20.328   8.713  36.780  1.00  0.00              
ATOM     99  C   VAL    38      18.979   8.679  36.067  1.00  0.00              
ATOM    100  O   VAL    38      17.928   8.596  36.703  1.00  0.00              
ATOM    101  N   LYS    39      19.019   8.756  34.742  1.00  0.00              
ATOM    102  CA  LYS    39      17.810   8.749  33.939  1.00  0.00              
ATOM    103  C   LYS    39      16.992   7.501  34.181  1.00  0.00              
ATOM    104  O   LYS    39      15.764   7.564  34.213  1.00  0.00              
ATOM    105  N   LYS    40      17.670   6.377  34.402  1.00  0.00              
ATOM    106  CA  LYS    40      16.980   5.117  34.669  1.00  0.00              
ATOM    107  C   LYS    40      16.385   5.100  36.073  1.00  0.00              
ATOM    108  O   LYS    40      15.360   4.454  36.315  1.00  0.00              
ATOM    109  N   GLU    41      17.037   5.796  37.002  1.00  0.00              
ATOM    110  CA  GLU    41      16.539   5.879  38.367  1.00  0.00              
ATOM    111  C   GLU    41      15.213   6.615  38.321  1.00  0.00              
ATOM    112  O   GLU    41      14.222   6.159  38.901  1.00  0.00              
ATOM    113  N   ALA    42      15.189   7.721  37.580  1.00  0.00              
ATOM    114  CA  ALA    42      13.996   8.546  37.443  1.00  0.00              
ATOM    115  C   ALA    42      12.832   7.843  36.736  1.00  0.00              
ATOM    116  O   ALA    42      11.672   8.052  37.094  1.00  0.00              
ATOM    117  N   LYS    43      13.136   7.049  35.711  1.00  0.00              
ATOM    118  CA  LYS    43      12.105   6.311  34.982  1.00  0.00              
ATOM    119  C   LYS    43      11.427   5.344  35.951  1.00  0.00              
ATOM    120  O   LYS    43      10.197   5.318  36.064  1.00  0.00              
ATOM    121  N   GLN    44      12.246   4.584  36.676  1.00  0.00              
ATOM    122  CA  GLN    44      11.769   3.617  37.661  1.00  0.00              
ATOM    123  C   GLN    44      10.867   4.308  38.689  1.00  0.00              
ATOM    124  O   GLN    44       9.887   3.724  39.150  1.00  0.00              
ATOM    125  N   LYS    45      11.185   5.557  39.029  1.00  0.00              
ATOM    126  CA  LYS    45      10.399   6.317  40.001  1.00  0.00              
ATOM    127  C   LYS    45       9.309   7.142  39.365  1.00  0.00              
ATOM    128  O   LYS    45       8.673   7.960  40.031  1.00  0.00              
ATOM    129  N   ALA    46       9.125   6.963  38.064  1.00  0.00              
ATOM    130  CA  ALA    46       8.094   7.698  37.363  1.00  0.00              
ATOM    131  C   ALA    46       8.358   9.188  37.280  1.00  0.00              
ATOM    132  O   ALA    46       7.443   9.962  37.004  1.00  0.00              
ATOM    133  N   LYS    52      10.904   7.196  27.137  1.00  0.00              
ATOM    134  CA  LYS    52      11.610   7.716  25.972  1.00  0.00              
ATOM    135  C   LYS    52      11.849   9.200  26.221  1.00  0.00              
ATOM    136  O   LYS    52      11.531  10.043  25.386  1.00  0.00              
ATOM    137  N   ASP    53      12.427   9.518  27.370  1.00  0.00              
ATOM    138  CA  ASP    53      12.655  10.910  27.714  1.00  0.00              
ATOM    139  C   ASP    53      14.006  11.111  28.377  1.00  0.00              
ATOM    140  O   ASP    53      14.471  10.259  29.135  1.00  0.00              
ATOM    141  N   TYR    54      14.654  12.223  28.051  1.00  0.00              
ATOM    142  CA  TYR    54      15.947  12.532  28.631  1.00  0.00              
ATOM    143  C   TYR    54      15.767  13.599  29.698  1.00  0.00              
ATOM    144  O   TYR    54      14.709  14.239  29.786  1.00  0.00              
ATOM    145  N   THR    55      16.783  13.756  30.538  1.00  0.00              
ATOM    146  CA  THR    55      16.747  14.748  31.585  1.00  0.00              
ATOM    147  C   THR    55      17.224  16.007  30.886  1.00  0.00              
ATOM    148  O   THR    55      18.378  16.096  30.501  1.00  0.00              
ATOM    149  N   GLN    56      16.311  16.934  30.632  1.00  0.00              
ATOM    150  CA  GLN    56      16.684  18.172  29.967  1.00  0.00              
ATOM    151  C   GLN    56      17.791  18.906  30.724  1.00  0.00              
ATOM    152  O   GLN    56      18.804  19.287  30.127  1.00  0.00              
ATOM    153  N   ASP    57      17.598  19.088  32.030  1.00  0.00              
ATOM    154  CA  ASP    57      18.571  19.769  32.888  1.00  0.00              
ATOM    155  C   ASP    57      18.176  19.617  34.356  1.00  0.00              
ATOM    156  O   ASP    57      17.079  19.144  34.676  1.00  0.00              
ATOM    157  N   CYS    60      16.924  25.097  39.162  1.00  0.00              
ATOM    158  CA  CYS    60      16.417  25.528  40.465  1.00  0.00              
ATOM    159  C   CYS    60      15.106  24.847  40.870  1.00  0.00              
ATOM    160  O   CYS    60      15.014  24.281  41.944  1.00  0.00              
ATOM    161  N   VAL    61      14.110  24.872  39.990  1.00  0.00              
ATOM    162  CA  VAL    61      12.790  24.273  40.246  1.00  0.00              
ATOM    163  C   VAL    61      12.823  22.770  40.543  1.00  0.00              
ATOM    164  O   VAL    61      11.953  22.237  41.241  1.00  0.00              
ATOM    165  N   GLY    62      13.829  22.092  40.008  1.00  0.00              
ATOM    166  CA  GLY    62      13.967  20.660  40.202  1.00  0.00              
ATOM    167  C   GLY    62      14.355  20.340  41.641  1.00  0.00              
ATOM    168  O   GLY    62      13.706  19.527  42.307  1.00  0.00              
ATOM    169  N   CYS    63      15.407  21.003  42.115  1.00  0.00              
ATOM    170  CA  CYS    63      15.910  20.819  43.470  1.00  0.00              
ATOM    171  C   CYS    63      15.084  21.547  44.522  1.00  0.00              
ATOM    172  O   CYS    63      14.957  21.071  45.647  1.00  0.00              
ATOM    173  N   HIS    64      14.506  22.686  44.157  1.00  0.00              
ATOM    174  CA  HIS    64      13.740  23.470  45.112  1.00  0.00              
ATOM    175  C   HIS    64      12.233  23.327  45.175  1.00  0.00              
ATOM    176  O   HIS    64      11.575  24.094  45.868  1.00  0.00              
ATOM    177  N   VAL    65      11.683  22.362  44.452  1.00  0.00              
ATOM    178  CA  VAL    65      10.247  22.103  44.474  1.00  0.00              
ATOM    179  C   VAL    65      10.029  20.637  44.117  1.00  0.00              
ATOM    180  O   VAL    65       9.769  19.823  45.000  1.00  0.00              
ATOM    181  N   ASP    66      10.170  20.296  42.834  1.00  0.00              
ATOM    182  CA  ASP    66       9.977  18.915  42.387  1.00  0.00              
ATOM    183  C   ASP    66      10.860  18.520  41.212  1.00  0.00              
ATOM    184  O   ASP    66      11.032  19.288  40.271  1.00  0.00              
ATOM    185  N   GLY    69       7.094  20.350  35.716  1.00  0.00              
ATOM    186  CA  GLY    69       6.689  21.033  34.486  1.00  0.00              
ATOM    187  C   GLY    69       5.987  22.361  34.778  1.00  0.00              
ATOM    188  O   GLY    69       6.502  23.441  34.494  1.00  0.00              
ATOM    189  N   GLN    70       4.803  22.248  35.360  1.00  0.00              
ATOM    190  CA  GLN    70       3.962  23.390  35.706  1.00  0.00              
ATOM    191  C   GLN    70       4.535  24.371  36.735  1.00  0.00              
ATOM    192  O   GLN    70       5.606  24.151  37.306  1.00  0.00              
ATOM    193  N   LYS    71       3.781  25.444  36.968  1.00  0.00              
ATOM    194  CA  LYS    71       4.141  26.507  37.902  1.00  0.00              
ATOM    195  C   LYS    71       4.238  26.032  39.340  1.00  0.00              
ATOM    196  O   LYS    71       3.531  25.111  39.755  1.00  0.00              
ATOM    197  N   GLY    72       5.065  26.724  40.110  1.00  0.00              
ATOM    198  CA  GLY    72       5.272  26.434  41.517  1.00  0.00              
ATOM    199  C   GLY    72       4.911  27.696  42.291  1.00  0.00              
ATOM    200  O   GLY    72       5.147  28.814  41.825  1.00  0.00              
ATOM    201  N   GLY    73       4.267  27.512  43.437  1.00  0.00              
ATOM    202  CA  GLY    73       3.880  28.624  44.293  1.00  0.00              
ATOM    203  C   GLY    73       5.047  28.833  45.241  1.00  0.00              
ATOM    204  O   GLY    73       5.341  27.978  46.066  1.00  0.00              
ATOM    205  N   GLU    77       5.424  26.189  47.996  1.00  0.00              
ATOM    206  CA  GLU    77       6.107  25.076  47.344  1.00  0.00              
ATOM    207  C   GLU    77       7.617  24.945  47.492  1.00  0.00              
ATOM    208  O   GLU    77       8.152  23.856  47.306  1.00  0.00              
ATOM    209  N   SER    78       8.306  26.034  47.813  1.00  0.00              
ATOM    210  CA  SER    78       9.762  25.994  47.962  1.00  0.00              
ATOM    211  C   SER    78      10.283  25.135  49.126  1.00  0.00              
ATOM    212  O   SER    78       9.778  25.200  50.251  1.00  0.00              
ATOM    213  N   PRO    79      11.322  24.355  48.849  1.00  0.00              
ATOM    214  CA  PRO    79      11.940  23.495  49.854  1.00  0.00              
ATOM    215  C   PRO    79      13.452  23.660  49.773  1.00  0.00              
ATOM    216  O   PRO    79      13.967  24.291  48.850  1.00  0.00              
ATOM    217  N   LYS    80      14.146  23.098  50.758  1.00  0.00              
ATOM    218  CA  LYS    80      15.605  23.104  50.804  1.00  0.00              
ATOM    219  C   LYS    80      15.996  21.649  50.537  1.00  0.00              
ATOM    220  O   LYS    80      15.586  20.750  51.268  1.00  0.00              
ATOM    221  N   PRO    81      16.778  21.400  49.478  1.00  0.00              
ATOM    222  CA  PRO    81      17.222  20.055  49.096  1.00  0.00              
ATOM    223  C   PRO    81      18.045  19.309  50.149  1.00  0.00              
ATOM    224  O   PRO    81      19.175  19.702  50.458  1.00  0.00              
END
