REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0061AL009_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0061  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0061, Protein HDEA  
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  2 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1efu_B 
ATOM      1  N   LYS    10      70.879  17.490  44.738  1.00  0.00              
ATOM      2  CA  LYS    10      70.328  18.646  45.398  1.00  0.00              
ATOM      3  C   LYS    10      69.964  19.660  44.343  1.00  0.00              
ATOM      4  O   LYS    10      70.786  19.988  43.497  1.00  0.00              
ATOM      5  N   LYS    11      68.717  20.117  44.379  1.00  0.00              
ATOM      6  CA  LYS    11      68.228  21.099  43.425  1.00  0.00              
ATOM      7  C   LYS    11      67.624  22.302  44.124  1.00  0.00              
ATOM      8  O   LYS    11      67.043  22.187  45.208  1.00  0.00              
ATOM      9  N   PRO    12      67.771  23.467  43.507  1.00  0.00              
ATOM     10  CA  PRO    12      67.251  24.706  44.063  1.00  0.00              
ATOM     11  C   PRO    12      66.375  25.426  43.058  1.00  0.00              
ATOM     12  O   PRO    12      66.683  25.467  41.868  1.00  0.00              
ATOM     13  N   VAL    13      65.246  25.932  43.532  1.00  0.00              
ATOM     14  CA  VAL    13      64.345  26.707  42.694  1.00  0.00              
ATOM     15  C   VAL    13      64.207  28.025  43.461  1.00  0.00              
ATOM     16  O   VAL    13      64.154  28.028  44.698  1.00  0.00              
ATOM     17  N   ASN    14      64.208  29.141  42.742  1.00  0.00              
ATOM     18  CA  ASN    14      64.165  30.451  43.382  1.00  0.00              
ATOM     19  C   ASN    14      63.336  31.478  42.621  1.00  0.00              
ATOM     20  O   ASN    14      63.218  31.395  41.401  1.00  0.00              
ATOM     21  N   SER    15      62.778  32.453  43.339  1.00  0.00              
ATOM     22  CA  SER    15      62.017  33.523  42.703  1.00  0.00              
ATOM     23  C   SER    15      62.557  34.876  43.136  1.00  0.00              
ATOM     24  O   SER    15      62.655  35.151  44.333  1.00  0.00              
ATOM     25  N   TRP    16      62.948  35.691  42.158  1.00  0.00              
ATOM     26  CA  TRP    16      63.455  37.043  42.394  1.00  0.00              
ATOM     27  C   TRP    16      62.559  37.977  41.591  1.00  0.00              
ATOM     28  O   TRP    16      62.437  37.860  40.363  1.00  0.00              
ATOM     29  N   THR    17      61.941  38.911  42.299  1.00  0.00              
ATOM     30  CA  THR    17      61.004  39.845  41.696  1.00  0.00              
ATOM     31  C   THR    17      61.488  41.256  41.411  1.00  0.00              
ATOM     32  O   THR    17      62.358  41.792  42.099  1.00  0.00              
ATOM     33  N   CYS    18      60.841  41.869  40.429  1.00  0.00              
ATOM     34  CA  CYS    18      61.103  43.241  40.024  1.00  0.00              
ATOM     35  C   CYS    18      59.740  43.799  39.579  1.00  0.00              
ATOM     36  O   CYS    18      58.735  43.093  39.623  1.00  0.00              
ATOM     37  N   ASP    20      59.026  43.571  33.210  1.00  0.00              
ATOM     38  CA  ASP    20      59.753  42.518  32.503  1.00  0.00              
ATOM     39  C   ASP    20      61.009  43.030  31.806  1.00  0.00              
ATOM     40  O   ASP    20      61.971  42.282  31.622  1.00  0.00              
ATOM     41  N   PHE    21      60.990  44.299  31.406  1.00  0.00              
ATOM     42  CA  PHE    21      62.144  44.905  30.757  1.00  0.00              
ATOM     43  C   PHE    21      63.319  44.716  31.711  1.00  0.00              
ATOM     44  O   PHE    21      64.430  44.429  31.286  1.00  0.00              
ATOM     45  N   LEU    22      63.064  44.837  33.008  1.00  0.00              
ATOM     46  CA  LEU    22      64.134  44.652  33.987  1.00  0.00              
ATOM     47  C   LEU    22      64.427  43.171  34.237  1.00  0.00              
ATOM     48  O   LEU    22      65.563  42.794  34.501  1.00  0.00              
ATOM     49  N   ALA    23      63.408  42.330  34.141  1.00  0.00              
ATOM     50  CA  ALA    23      63.599  40.907  34.348  1.00  0.00              
ATOM     51  C   ALA    23      64.511  40.387  33.246  1.00  0.00              
ATOM     52  O   ALA    23      65.278  39.452  33.455  1.00  0.00              
ATOM     53  N   GLU    26      70.380  42.214  31.931  1.00  0.00              
ATOM     54  CA  GLU    26      71.590  41.448  32.263  1.00  0.00              
ATOM     55  C   GLU    26      72.020  41.617  33.714  1.00  0.00              
ATOM     56  O   GLU    26      72.407  40.657  34.372  1.00  0.00              
ATOM     57  N   SER    27      71.943  42.845  34.213  1.00  0.00              
ATOM     58  CA  SER    27      72.307  43.097  35.592  1.00  0.00              
ATOM     59  C   SER    27      71.392  42.344  36.539  1.00  0.00              
ATOM     60  O   SER    27      71.846  41.762  37.531  1.00  0.00              
ATOM     61  N   PHE    28      70.101  42.345  36.225  1.00  0.00              
ATOM     62  CA  PHE    28      69.103  41.653  37.034  1.00  0.00              
ATOM     63  C   PHE    28      69.372  40.150  36.945  1.00  0.00              
ATOM     64  O   PHE    28      69.358  39.457  37.970  1.00  0.00              
ATOM     65  N   GLN    29      69.650  39.663  35.728  1.00  0.00              
ATOM     66  CA  GLN    29      69.958  38.244  35.480  1.00  0.00              
ATOM     67  C   GLN    29      71.180  37.845  36.289  1.00  0.00              
ATOM     68  O   GLN    29      71.189  36.813  36.968  1.00  0.00              
ATOM     69  N   PRO    30      72.208  38.687  36.204  1.00  0.00              
ATOM     70  CA  PRO    30      73.469  38.502  36.912  1.00  0.00              
ATOM     71  C   PRO    30      73.207  38.400  38.420  1.00  0.00              
ATOM     72  O   PRO    30      73.773  37.535  39.097  1.00  0.00              
ATOM     73  N   THR    31      72.322  39.254  38.934  1.00  0.00              
ATOM     74  CA  THR    31      71.950  39.239  40.358  1.00  0.00              
ATOM     75  C   THR    31      71.222  37.938  40.730  1.00  0.00              
ATOM     76  O   THR    31      71.641  37.225  41.640  1.00  0.00              
ATOM     77  N   ALA    32      70.154  37.615  40.009  1.00  0.00              
ATOM     78  CA  ALA    32      69.403  36.399  40.284  1.00  0.00              
ATOM     79  C   ALA    32      70.265  35.144  40.143  1.00  0.00              
ATOM     80  O   ALA    32      70.139  34.208  40.936  1.00  0.00              
ATOM     81  N   VAL    33      71.136  35.114  39.141  1.00  0.00              
ATOM     82  CA  VAL    33      72.016  33.962  38.932  1.00  0.00              
ATOM     83  C   VAL    33      73.007  33.775  40.074  1.00  0.00              
ATOM     84  O   VAL    33      73.306  32.648  40.474  1.00  0.00              
ATOM     85  N   GLY    34      73.502  34.885  40.605  1.00  0.00              
ATOM     86  CA  GLY    34      74.457  34.863  41.706  1.00  0.00              
ATOM     87  C   GLY    34      73.772  34.360  42.987  1.00  0.00              
ATOM     88  O   GLY    34      74.380  33.628  43.780  1.00  0.00              
ATOM     89  N   PHE    35      72.510  34.754  43.178  1.00  0.00              
ATOM     90  CA  PHE    35      71.706  34.342  44.337  1.00  0.00              
ATOM     91  C   PHE    35      71.429  32.844  44.228  1.00  0.00              
ATOM     92  O   PHE    35      71.485  32.113  45.222  1.00  0.00              
ATOM     93  N   ALA    36      71.140  32.399  43.006  1.00  0.00              
ATOM     94  CA  ALA    36      70.878  30.989  42.698  1.00  0.00              
ATOM     95  C   ALA    36      72.109  30.114  43.012  1.00  0.00              
ATOM     96  O   ALA    36      72.006  29.104  43.709  1.00  0.00              
ATOM     97  N   GLU    37      73.264  30.493  42.463  1.00  0.00              
ATOM     98  CA  GLU    37      74.509  29.757  42.679  1.00  0.00              
ATOM     99  C   GLU    37      74.823  29.617  44.160  1.00  0.00              
ATOM    100  O   GLU    37      75.151  28.530  44.639  1.00  0.00              
ATOM    101  N   ALA    38      74.756  30.733  44.877  1.00  0.00              
ATOM    102  CA  ALA    38      75.037  30.729  46.307  1.00  0.00              
ATOM    103  C   ALA    38      74.103  29.802  47.080  1.00  0.00              
ATOM    104  O   ALA    38      74.528  29.141  48.027  1.00  0.00              
ATOM    105  N   LEU    39      72.837  29.750  46.671  1.00  0.00              
ATOM    106  CA  LEU    39      71.841  28.911  47.326  1.00  0.00              
ATOM    107  C   LEU    39      72.138  27.431  47.112  1.00  0.00              
ATOM    108  O   LEU    39      71.920  26.606  48.004  1.00  0.00              
ATOM    109  N   ASN    40      72.645  27.093  45.931  1.00  0.00              
ATOM    110  CA  ASN    40      73.002  25.709  45.625  1.00  0.00              
ATOM    111  C   ASN    40      74.290  25.365  46.357  1.00  0.00              
ATOM    112  O   ASN    40      74.365  24.359  47.059  1.00  0.00              
ATOM    113  N   ASN    41      75.273  26.254  46.242  1.00  0.00              
ATOM    114  CA  ASN    41      76.582  26.071  46.863  1.00  0.00              
ATOM    115  C   ASN    41      76.495  25.840  48.355  1.00  0.00              
ATOM    116  O   ASN    41      77.098  24.904  48.879  1.00  0.00              
ATOM    117  N   ALA    48      69.494  38.133  53.703  1.00  0.00              
ATOM    118  CA  ALA    48      70.511  38.779  54.530  1.00  0.00              
ATOM    119  C   ALA    48      71.865  38.830  53.844  1.00  0.00              
ATOM    120  O   ALA    48      72.557  39.851  53.880  1.00  0.00              
ATOM    121  N   VAL    49      72.218  37.740  53.181  1.00  0.00              
ATOM    122  CA  VAL    49      73.496  37.638  52.494  1.00  0.00              
ATOM    123  C   VAL    49      73.626  38.558  51.274  1.00  0.00              
ATOM    124  O   VAL    49      74.713  39.066  50.985  1.00  0.00              
ATOM    125  N   LEU    50      72.517  38.791  50.577  1.00  0.00              
ATOM    126  CA  LEU    50      72.520  39.617  49.372  1.00  0.00              
ATOM    127  C   LEU    50      71.913  41.007  49.501  1.00  0.00              
ATOM    128  O   LEU    50      71.789  41.729  48.504  1.00  0.00              
ATOM    129  N   ASP    51      71.603  41.414  50.726  1.00  0.00              
ATOM    130  CA  ASP    51      70.994  42.718  50.979  1.00  0.00              
ATOM    131  C   ASP    51      71.784  43.914  50.425  1.00  0.00              
ATOM    132  O   ASP    51      71.217  44.767  49.733  1.00  0.00              
ATOM    133  N   VAL    52      73.086  43.972  50.692  1.00  0.00              
ATOM    134  CA  VAL    52      73.923  45.072  50.196  1.00  0.00              
ATOM    135  C   VAL    52      73.869  45.156  48.671  1.00  0.00              
ATOM    136  O   VAL    52      73.587  46.214  48.111  1.00  0.00              
ATOM    137  N   GLN    53      74.136  44.036  48.007  1.00  0.00              
ATOM    138  CA  GLN    53      74.103  43.963  46.545  1.00  0.00              
ATOM    139  C   GLN    53      72.727  44.331  45.982  1.00  0.00              
ATOM    140  O   GLN    53      72.630  45.034  44.978  1.00  0.00              
ATOM    141  N   GLY    54      71.669  43.833  46.619  1.00  0.00              
ATOM    142  CA  GLY    54      70.297  44.107  46.189  1.00  0.00              
ATOM    143  C   GLY    54      70.033  45.604  46.229  1.00  0.00              
ATOM    144  O   GLY    54      69.429  46.155  45.311  1.00  0.00              
ATOM    145  N   ILE    55      70.497  46.255  47.295  1.00  0.00              
ATOM    146  CA  ILE    55      70.332  47.695  47.467  1.00  0.00              
ATOM    147  C   ILE    55      71.104  48.472  46.400  1.00  0.00              
ATOM    148  O   ILE    55      70.626  49.488  45.882  1.00  0.00              
ATOM    149  N   ALA    56      72.295  47.988  46.068  1.00  0.00              
ATOM    150  CA  ALA    56      73.115  48.626  45.046  1.00  0.00              
ATOM    151  C   ALA    56      72.390  48.533  43.705  1.00  0.00              
ATOM    152  O   ALA    56      72.237  49.532  43.010  1.00  0.00              
ATOM    153  N   THR    57      71.931  47.334  43.356  1.00  0.00              
ATOM    154  CA  THR    57      71.205  47.093  42.105  1.00  0.00              
ATOM    155  C   THR    57      69.939  47.951  42.035  1.00  0.00              
ATOM    156  O   THR    57      69.688  48.648  41.042  1.00  0.00              
ATOM    157  N   VAL    58      69.146  47.916  43.097  1.00  0.00              
ATOM    158  CA  VAL    58      67.923  48.708  43.145  1.00  0.00              
ATOM    159  C   VAL    58      68.272  50.177  42.913  1.00  0.00              
ATOM    160  O   VAL    58      67.590  50.869  42.157  1.00  0.00              
ATOM    161  N   THR    59      69.369  50.632  43.507  1.00  0.00              
ATOM    162  CA  THR    59      69.793  52.020  43.354  1.00  0.00              
ATOM    163  C   THR    59      70.180  52.391  41.921  1.00  0.00              
ATOM    164  O   THR    59      70.155  53.573  41.561  1.00  0.00              
ATOM    165  N   PRO    60      70.552  51.406  41.107  1.00  0.00              
ATOM    166  CA  PRO    60      70.906  51.704  39.722  1.00  0.00              
ATOM    167  C   PRO    60      69.836  51.291  38.709  1.00  0.00              
ATOM    168  O   PRO    60      69.855  51.748  37.567  1.00  0.00              
ATOM    169  N   ALA    61      68.892  50.456  39.139  1.00  0.00              
ATOM    170  CA  ALA    61      67.800  50.005  38.273  1.00  0.00              
ATOM    171  C   ALA    61      66.511  50.803  38.521  1.00  0.00              
ATOM    172  O   ALA    61      65.684  50.972  37.618  1.00  0.00              
ATOM    173  N   THR    67      63.291  42.070  44.880  1.00  0.00              
ATOM    174  CA  THR    67      63.153  41.317  46.124  1.00  0.00              
ATOM    175  C   THR    67      63.387  39.813  45.916  1.00  0.00              
ATOM    176  O   THR    67      62.942  39.247  44.919  1.00  0.00              
ATOM    177  N   GLN    68      64.198  39.206  46.782  1.00  0.00              
ATOM    178  CA  GLN    68      64.455  37.764  46.724  1.00  0.00              
ATOM    179  C   GLN    68      63.253  37.245  47.499  1.00  0.00              
ATOM    180  O   GLN    68      63.215  37.300  48.725  1.00  0.00              
ATOM    181  N   ASP    69      62.259  36.767  46.768  1.00  0.00              
ATOM    182  CA  ASP    69      61.016  36.327  47.371  1.00  0.00              
ATOM    183  C   ASP    69      60.956  34.971  48.063  1.00  0.00              
ATOM    184  O   ASP    69      60.426  34.847  49.168  1.00  0.00              
ATOM    185  N   LYS    70      61.452  33.939  47.406  1.00  0.00              
ATOM    186  CA  LYS    70      61.393  32.624  47.992  1.00  0.00              
ATOM    187  C   LYS    70      62.402  31.713  47.339  1.00  0.00              
ATOM    188  O   LYS    70      62.917  32.015  46.268  1.00  0.00              
ATOM    189  N   GLN    71      62.679  30.600  48.010  1.00  0.00              
ATOM    190  CA  GLN    71      63.641  29.602  47.553  1.00  0.00              
ATOM    191  C   GLN    71      63.304  28.305  48.252  1.00  0.00              
ATOM    192  O   GLN    71      62.799  28.313  49.378  1.00  0.00              
ATOM    193  N   ALA    72      63.523  27.195  47.564  1.00  0.00              
ATOM    194  CA  ALA    72      63.254  25.878  48.132  1.00  0.00              
ATOM    195  C   ALA    72      64.210  24.876  47.489  1.00  0.00              
ATOM    196  O   ALA    72      64.736  25.119  46.395  1.00  0.00              
ATOM    197  N   ASN    73      64.443  23.761  48.168  1.00  0.00              
ATOM    198  CA  ASN    73      65.320  22.742  47.627  1.00  0.00              
ATOM    199  C   ASN    73      64.541  21.469  47.426  1.00  0.00              
ATOM    200  O   ASN    73      63.579  21.213  48.151  1.00  0.00              
ATOM    201  N   PHE    74      64.910  20.713  46.400  1.00  0.00              
ATOM    202  CA  PHE    74      64.293  19.429  46.130  1.00  0.00              
ATOM    203  C   PHE    74      65.478  18.487  46.138  1.00  0.00              
ATOM    204  O   PHE    74      66.532  18.812  45.584  1.00  0.00              
ATOM    205  N   LYS    75      65.327  17.362  46.825  1.00  0.00              
ATOM    206  CA  LYS    75      66.382  16.369  46.896  1.00  0.00              
ATOM    207  C   LYS    75      65.854  15.050  46.365  1.00  0.00              
ATOM    208  O   LYS    75      64.691  14.713  46.576  1.00  0.00              
ATOM    209  N   VAL    78      67.598  11.089  41.151  1.00  0.00              
ATOM    210  CA  VAL    78      67.828  11.706  39.840  1.00  0.00              
ATOM    211  C   VAL    78      67.028  13.017  39.846  1.00  0.00              
ATOM    212  O   VAL    78      65.829  12.999  40.127  1.00  0.00              
ATOM    213  N   LYS    79      67.694  14.143  39.584  1.00  0.00              
ATOM    214  CA  LYS    79      67.041  15.462  39.547  1.00  0.00              
ATOM    215  C   LYS    79      66.995  16.082  38.149  1.00  0.00              
ATOM    216  O   LYS    79      67.973  16.046  37.402  1.00  0.00              
ATOM    217  N   GLY    80      65.858  16.684  37.821  1.00  0.00              
ATOM    218  CA  GLY    80      65.670  17.322  36.530  1.00  0.00              
ATOM    219  C   GLY    80      64.951  18.648  36.714  1.00  0.00              
ATOM    220  O   GLY    80      64.357  18.916  37.764  1.00  0.00              
ATOM    221  N   GLU    81      65.050  19.507  35.714  1.00  0.00              
ATOM    222  CA  GLU    81      64.414  20.803  35.784  1.00  0.00              
ATOM    223  C   GLU    81      63.866  21.225  34.439  1.00  0.00              
ATOM    224  O   GLU    81      64.195  20.662  33.397  1.00  0.00              
ATOM    225  N   TRP    82      62.998  22.213  34.470  1.00  0.00              
ATOM    226  CA  TRP    82      62.422  22.732  33.256  1.00  0.00              
ATOM    227  C   TRP    82      62.015  24.175  33.531  1.00  0.00              
ATOM    228  O   TRP    82      61.386  24.475  34.556  1.00  0.00              
ATOM    229  N   ASP    83      62.502  25.071  32.682  1.00  0.00              
ATOM    230  CA  ASP    83      62.182  26.486  32.775  1.00  0.00              
ATOM    231  C   ASP    83      61.335  26.818  31.565  1.00  0.00              
ATOM    232  O   ASP    83      61.734  26.539  30.433  1.00  0.00              
ATOM    233  N   LYS    84      60.120  27.289  31.795  1.00  0.00              
ATOM    234  CA  LYS    84      59.258  27.684  30.688  1.00  0.00              
ATOM    235  C   LYS    84      59.423  29.193  30.663  1.00  0.00              
ATOM    236  O   LYS    84      58.622  29.933  31.244  1.00  0.00              
END
