REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0061AL009_3 
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1l92 
ATOM      1  N   ALA     3      20.769   6.656   6.192  1.00  0.00              
ATOM      2  CA  ALA     3      22.068   6.024   6.221  1.00  0.00              
ATOM      3  C   ALA     3      22.051   4.522   6.497  1.00  0.00              
ATOM      4  O   ALA     3      22.822   3.766   5.925  1.00  0.00              
ATOM      5  N   GLN     4      21.217   4.118   7.428  1.00  0.00              
ATOM      6  CA  GLN     4      21.134   2.760   7.862  1.00  0.00              
ATOM      7  C   GLN     4      21.051   1.718   6.742  1.00  0.00              
ATOM      8  O   GLN     4      21.774   0.719   6.730  1.00  0.00              
ATOM      9  N   LYS     5      20.153   1.932   5.805  1.00  0.00              
ATOM     10  CA  LYS     5      19.972   1.024   4.695  1.00  0.00              
ATOM     11  C   LYS     5      21.226   0.910   3.869  1.00  0.00              
ATOM     12  O   LYS     5      21.589  -0.152   3.411  1.00  0.00              
ATOM     13  N   ALA     6      21.923   2.026   3.682  1.00  0.00              
ATOM     14  CA  ALA     6      23.161   1.975   2.919  1.00  0.00              
ATOM     15  C   ALA     6      24.229   1.140   3.638  1.00  0.00              
ATOM     16  O   ALA     6      24.847   0.231   3.098  1.00  0.00              
ATOM     17  N   ALA     7      24.443   1.506   4.907  1.00  0.00              
ATOM     18  CA  ALA     7      25.387   0.844   5.776  1.00  0.00              
ATOM     19  C   ALA     7      25.123  -0.673   5.777  1.00  0.00              
ATOM     20  O   ALA     7      26.039  -1.497   5.563  1.00  0.00              
ATOM     21  N   ASP     8      23.835  -1.054   6.012  1.00  0.00              
ATOM     22  CA  ASP     8      23.437  -2.461   6.058  1.00  0.00              
ATOM     23  C   ASP     8      23.784  -3.202   4.805  1.00  0.00              
ATOM     24  O   ASP     8      24.098  -4.378   4.837  1.00  0.00              
ATOM     25  N   ASN     9      23.714  -2.515   3.686  1.00  0.00              
ATOM     26  CA  ASN     9      23.998  -3.179   2.438  1.00  0.00              
ATOM     27  C   ASN     9      25.469  -3.387   2.127  1.00  0.00              
ATOM     28  O   ASN     9      25.820  -4.140   1.217  1.00  0.00              
ATOM     29  N   THR    17      32.377  -4.976   4.999  1.00  0.00              
ATOM     30  CA  THR    17      33.057  -4.336   6.139  1.00  0.00              
ATOM     31  C   THR    17      34.017  -3.154   5.816  1.00  0.00              
ATOM     32  O   THR    17      34.071  -2.141   6.530  1.00  0.00              
ATOM     33  N   CYS    18      34.724  -3.267   4.699  1.00  0.00              
ATOM     34  CA  CYS    18      35.652  -2.198   4.329  1.00  0.00              
ATOM     35  C   CYS    18      34.879  -0.933   3.981  1.00  0.00              
ATOM     36  O   CYS    18      35.164   0.182   4.451  1.00  0.00              
ATOM     37  N   GLU    19      33.877  -1.107   3.129  1.00  0.00              
ATOM     38  CA  GLU    19      33.072   0.044   2.708  1.00  0.00              
ATOM     39  C   GLU    19      32.326   0.652   3.854  1.00  0.00              
ATOM     40  O   GLU    19      32.137   1.865   3.854  1.00  0.00              
ATOM     41  N   ASP    20      31.906  -0.156   4.844  1.00  0.00              
ATOM     42  CA  ASP    20      31.240   0.403   6.052  1.00  0.00              
ATOM     43  C   ASP    20      32.197   1.423   6.764  1.00  0.00              
ATOM     44  O   ASP    20      31.795   2.488   7.181  1.00  0.00              
ATOM     45  N   PHE    21      33.492   1.076   6.842  1.00  0.00              
ATOM     46  CA  PHE    21      34.482   1.967   7.402  1.00  0.00              
ATOM     47  C   PHE    21      34.521   3.325   6.632  1.00  0.00              
ATOM     48  O   PHE    21      34.719   4.417   7.229  1.00  0.00              
ATOM     49  N   LEU    22      34.401   3.253   5.291  1.00  0.00              
ATOM     50  CA  LEU    22      34.422   4.467   4.465  1.00  0.00              
ATOM     51  C   LEU    22      33.257   5.401   4.790  1.00  0.00              
ATOM     52  O   LEU    22      33.397   6.624   4.853  1.00  0.00              
ATOM     53  N   ALA    23      32.078   4.846   5.001  1.00  0.00              
ATOM     54  CA  ALA    23      30.965   5.720   5.337  1.00  0.00              
ATOM     55  C   ALA    23      31.076   6.235   6.764  1.00  0.00              
ATOM     56  O   ALA    23      30.677   7.380   7.060  1.00  0.00              
ATOM     57  N   VAL    24      31.700   5.459   7.663  1.00  0.00              
ATOM     58  CA  VAL    24      31.871   5.953   9.022  1.00  0.00              
ATOM     59  C   VAL    24      32.851   7.153   8.959  1.00  0.00              
ATOM     60  O   VAL    24      32.670   8.217   9.586  1.00  0.00              
ATOM     61  N   ASP    25      33.874   7.010   8.120  1.00  0.00              
ATOM     62  CA  ASP    25      34.864   8.091   7.974  1.00  0.00              
ATOM     63  C   ASP    25      34.156   9.365   7.515  1.00  0.00              
ATOM     64  O   ASP    25      34.356  10.411   8.128  1.00  0.00              
ATOM     65  N   GLU    26      33.301   9.297   6.475  1.00  0.00              
ATOM     66  CA  GLU    26      32.599  10.484   6.025  1.00  0.00              
ATOM     67  C   GLU    26      31.758  11.130   7.136  1.00  0.00              
ATOM     68  O   GLU    26      31.706  12.374   7.308  1.00  0.00              
ATOM     69  N   SER    27      31.058  10.273   7.896  1.00  0.00              
ATOM     70  CA  SER    27      30.183  10.771   8.946  1.00  0.00              
ATOM     71  C   SER    27      30.978  11.485  10.039  1.00  0.00              
ATOM     72  O   SER    27      30.637  12.531  10.527  1.00  0.00              
ATOM     73  N   PHE    28      32.094  10.905  10.417  1.00  0.00              
ATOM     74  CA  PHE    28      32.942  11.472  11.417  1.00  0.00              
ATOM     75  C   PHE    28      33.420  12.876  10.997  1.00  0.00              
ATOM     76  O   PHE    28      33.512  13.761  11.791  1.00  0.00              
ATOM     77  N   GLN    29      33.718  13.074   9.719  1.00  0.00              
ATOM     78  CA  GLN    29      34.215  14.339   9.187  1.00  0.00              
ATOM     79  C   GLN    29      33.127  15.345   8.930  1.00  0.00              
ATOM     80  O   GLN    29      33.294  16.520   9.131  1.00  0.00              
ATOM     81  N   PRO    30      32.028  14.923   8.391  1.00  0.00              
ATOM     82  CA  PRO    30      31.032  15.867   8.001  1.00  0.00              
ATOM     83  C   PRO    30      29.676  15.805   8.647  1.00  0.00              
ATOM     84  O   PRO    30      28.793  16.591   8.357  1.00  0.00              
ATOM     85  N   THR    31      29.529  14.901   9.581  1.00  0.00              
ATOM     86  CA  THR    31      28.294  14.747  10.292  1.00  0.00              
ATOM     87  C   THR    31      27.271  14.013   9.440  1.00  0.00              
ATOM     88  O   THR    31      27.334  14.012   8.216  1.00  0.00              
ATOM     89  N   ALA    32      26.327  13.432  10.133  1.00  0.00              
ATOM     90  CA  ALA    32      25.262  12.628   9.575  1.00  0.00              
ATOM     91  C   ALA    32      24.397  13.391   8.589  1.00  0.00              
ATOM     92  O   ALA    32      24.038  12.898   7.520  1.00  0.00              
ATOM     93  N   VAL    33      24.113  14.644   8.916  1.00  0.00              
ATOM     94  CA  VAL    33      23.306  15.453   8.052  1.00  0.00              
ATOM     95  C   VAL    33      23.934  15.632   6.674  1.00  0.00              
ATOM     96  O   VAL    33      23.283  15.456   5.615  1.00  0.00              
ATOM     97  N   GLY    34      25.239  15.953   6.733  1.00  0.00              
ATOM     98  CA  GLY    34      26.034  16.160   5.556  1.00  0.00              
ATOM     99  C   GLY    34      26.031  14.961   4.628  1.00  0.00              
ATOM    100  O   GLY    34      25.710  15.100   3.437  1.00  0.00              
ATOM    101  N   PHE    35      26.400  13.782   5.180  1.00  0.00              
ATOM    102  CA  PHE    35      26.471  12.570   4.381  1.00  0.00              
ATOM    103  C   PHE    35      25.089  12.202   3.820  1.00  0.00              
ATOM    104  O   PHE    35      24.935  11.882   2.633  1.00  0.00              
ATOM    105  N   ALA    36      24.079  12.300   4.684  1.00  0.00              
ATOM    106  CA  ALA    36      22.704  11.999   4.296  1.00  0.00              
ATOM    107  C   ALA    36      22.296  12.860   3.103  1.00  0.00              
ATOM    108  O   ALA    36      21.446  12.480   2.273  1.00  0.00              
ATOM    109  N   GLU    46      22.533  12.204  -1.551  1.00  0.00              
ATOM    110  CA  GLU    46      21.470  11.363  -2.048  1.00  0.00              
ATOM    111  C   GLU    46      21.777  10.465  -3.213  1.00  0.00              
ATOM    112  O   GLU    46      21.521   9.268  -3.144  1.00  0.00              
ATOM    113  N   ASP    47      22.282  11.055  -4.300  1.00  0.00              
ATOM    114  CA  ASP    47      22.601  10.261  -5.513  1.00  0.00              
ATOM    115  C   ASP    47      23.707   9.198  -5.342  1.00  0.00              
ATOM    116  O   ASP    47      23.611   8.055  -5.827  1.00  0.00              
ATOM    117  N   ALA    48      24.778   9.603  -4.661  1.00  0.00              
ATOM    118  CA  ALA    48      25.912   8.721  -4.399  1.00  0.00              
ATOM    119  C   ALA    48      25.468   7.578  -3.499  1.00  0.00              
ATOM    120  O   ALA    48      25.902   6.461  -3.688  1.00  0.00              
ATOM    121  N   VAL    49      24.642   7.876  -2.481  1.00  0.00              
ATOM    122  CA  VAL    49      24.156   6.853  -1.524  1.00  0.00              
ATOM    123  C   VAL    49      23.366   5.786  -2.291  1.00  0.00              
ATOM    124  O   VAL    49      23.471   4.593  -2.049  1.00  0.00              
ATOM    125  N   LEU    50      22.576   6.239  -3.237  1.00  0.00              
ATOM    126  CA  LEU    50      21.762   5.335  -4.046  1.00  0.00              
ATOM    127  C   LEU    50      22.637   4.460  -4.903  1.00  0.00              
ATOM    128  O   LEU    50      22.410   3.236  -5.034  1.00  0.00              
ATOM    129  N   ASP    51      23.714   5.067  -5.454  1.00  0.00              
ATOM    130  CA  ASP    51      24.642   4.281  -6.247  1.00  0.00              
ATOM    131  C   ASP    51      25.433   3.281  -5.387  1.00  0.00              
ATOM    132  O   ASP    51      25.732   2.146  -5.820  1.00  0.00              
ATOM    133  N   VAL    52      25.803   3.673  -4.150  1.00  0.00              
ATOM    134  CA  VAL    52      26.550   2.738  -3.307  1.00  0.00              
ATOM    135  C   VAL    52      25.607   1.513  -2.985  1.00  0.00              
ATOM    136  O   VAL    52      25.946   0.337  -3.036  1.00  0.00              
ATOM    137  N   GLN    53      24.367   1.822  -2.654  1.00  0.00              
ATOM    138  CA  GLN    53      23.412   0.796  -2.314  1.00  0.00              
ATOM    139  C   GLN    53      23.239  -0.215  -3.451  1.00  0.00              
ATOM    140  O   GLN    53      23.106  -1.425  -3.234  1.00  0.00              
ATOM    141  N   VAL    58      29.995   0.835  -8.090  1.00  0.00              
ATOM    142  CA  VAL    58      31.227   1.420  -7.511  1.00  0.00              
ATOM    143  C   VAL    58      31.875   2.555  -8.270  1.00  0.00              
ATOM    144  O   VAL    58      32.191   3.600  -7.685  1.00  0.00              
ATOM    145  N   THR    59      32.125   2.319  -9.541  1.00  0.00              
ATOM    146  CA  THR    59      32.755   3.310 -10.386  1.00  0.00              
ATOM    147  C   THR    59      31.867   4.525 -10.527  1.00  0.00              
ATOM    148  O   THR    59      32.325   5.642 -10.457  1.00  0.00              
ATOM    149  N   PRO    60      30.554   4.325 -10.689  1.00  0.00              
ATOM    150  CA  PRO    60      29.661   5.454 -10.844  1.00  0.00              
ATOM    151  C   PRO    60      29.557   6.295  -9.587  1.00  0.00              
ATOM    152  O   PRO    60      29.488   7.533  -9.625  1.00  0.00              
ATOM    153  N   ALA    61      29.504   5.605  -8.461  1.00  0.00              
ATOM    154  CA  ALA    61      29.427   6.303  -7.178  1.00  0.00              
ATOM    155  C   ALA    61      30.698   7.158  -6.943  1.00  0.00              
ATOM    156  O   ALA    61      30.608   8.254  -6.391  1.00  0.00              
ATOM    157  N   ILE    62      31.865   6.621  -7.315  1.00  0.00              
ATOM    158  CA  ILE    62      33.158   7.319  -7.135  1.00  0.00              
ATOM    159  C   ILE    62      33.189   8.632  -7.931  1.00  0.00              
ATOM    160  O   ILE    62      33.668   9.669  -7.451  1.00  0.00              
ATOM    161  N   VAL    63      32.684   8.566  -9.179  1.00  0.00              
ATOM    162  CA  VAL    63      32.584   9.728 -10.019  1.00  0.00              
ATOM    163  C   VAL    63      31.642  10.750  -9.379  1.00  0.00              
ATOM    164  O   VAL    63      31.978  11.893  -9.265  1.00  0.00              
ATOM    165  N   GLN    64      30.449  10.353  -8.935  1.00  0.00              
ATOM    166  CA  GLN    64      29.506  11.311  -8.341  1.00  0.00              
ATOM    167  C   GLN    64      30.025  11.887  -7.003  1.00  0.00              
ATOM    168  O   GLN    64      29.839  13.043  -6.623  1.00  0.00              
ATOM    169  N   ALA    65      30.698  11.065  -6.222  1.00  0.00              
ATOM    170  CA  ALA    65      31.186  11.559  -4.928  1.00  0.00              
ATOM    171  C   ALA    65      32.199  12.718  -5.127  1.00  0.00              
ATOM    172  O   ALA    65      32.371  13.596  -4.275  1.00  0.00              
ATOM    173  N   CYS    66      32.940  12.660  -6.235  1.00  0.00              
ATOM    174  CA  CYS    66      34.002  13.666  -6.516  1.00  0.00              
ATOM    175  C   CYS    66      33.438  15.047  -6.860  1.00  0.00              
ATOM    176  O   CYS    66      34.132  16.055  -6.783  1.00  0.00              
ATOM    177  N   GLN    68      31.753  19.790  -2.781  1.00  0.00              
ATOM    178  CA  GLN    68      32.657  20.732  -2.155  1.00  0.00              
ATOM    179  C   GLN    68      33.732  19.965  -1.340  1.00  0.00              
ATOM    180  O   GLN    68      34.903  20.331  -1.266  1.00  0.00              
ATOM    181  N   ASP    69      33.292  18.880  -0.665  1.00  0.00              
ATOM    182  CA  ASP    69      34.127  17.987   0.162  1.00  0.00              
ATOM    183  C   ASP    69      35.413  17.568  -0.588  1.00  0.00              
ATOM    184  O   ASP    69      36.538  17.693  -0.094  1.00  0.00              
ATOM    185  N   LYS    70      35.226  17.103  -1.832  1.00  0.00              
ATOM    186  CA  LYS    70      36.321  16.642  -2.642  1.00  0.00              
ATOM    187  C   LYS    70      37.193  17.824  -3.004  1.00  0.00              
ATOM    188  O   LYS    70      38.408  17.746  -2.996  1.00  0.00              
ATOM    189  N   GLN    71      36.564  18.934  -3.362  1.00  0.00              
ATOM    190  CA  GLN    71      37.349  20.148  -3.724  1.00  0.00              
ATOM    191  C   GLN    71      38.182  20.762  -2.576  1.00  0.00              
ATOM    192  O   GLN    71      39.300  21.262  -2.756  1.00  0.00              
ATOM    193  N   ALA    72      37.653  20.713  -1.375  1.00  0.00              
ATOM    194  CA  ALA    72      38.290  21.263  -0.205  1.00  0.00              
ATOM    195  C   ALA    72      39.390  20.385   0.373  1.00  0.00              
ATOM    196  O   ALA    72      40.424  20.899   0.771  1.00  0.00              
ATOM    197  N   LYS    75      40.889  17.321  -1.074  1.00  0.00              
ATOM    198  CA  LYS    75      41.061  16.333  -2.156  1.00  0.00              
ATOM    199  C   LYS    75      41.883  15.066  -1.798  1.00  0.00              
ATOM    200  O   LYS    75      41.518  14.009  -2.245  1.00  0.00              
ATOM    201  N   ASP    76      42.988  15.165  -1.028  1.00  0.00              
ATOM    202  CA  ASP    76      43.767  13.983  -0.736  1.00  0.00              
ATOM    203  C   ASP    76      42.997  12.963   0.133  1.00  0.00              
ATOM    204  O   ASP    76      43.020  11.777  -0.126  1.00  0.00              
ATOM    205  N   LYS    77      42.353  13.461   1.169  1.00  0.00              
ATOM    206  CA  LYS    77      41.551  12.625   2.029  1.00  0.00              
ATOM    207  C   LYS    77      40.296  12.073   1.276  1.00  0.00              
ATOM    208  O   LYS    77      39.941  10.882   1.403  1.00  0.00              
ATOM    209  N   VAL    78      39.558  12.952   0.531  1.00  0.00              
ATOM    210  CA  VAL    78      38.411  12.501  -0.230  1.00  0.00              
ATOM    211  C   VAL    78      38.852  11.343  -1.184  1.00  0.00              
ATOM    212  O   VAL    78      38.188  10.310  -1.274  1.00  0.00              
ATOM    213  N   LYS    79      39.981  11.496  -1.910  1.00  0.00              
ATOM    214  CA  LYS    79      40.494  10.463  -2.836  1.00  0.00              
ATOM    215  C   LYS    79      40.708   9.132  -2.154  1.00  0.00              
ATOM    216  O   LYS    79      40.425   8.067  -2.707  1.00  0.00              
ATOM    217  N   GLY    80      41.249   9.196  -0.944  1.00  0.00              
ATOM    218  CA  GLY    80      41.468   7.953  -0.202  1.00  0.00              
ATOM    219  C   GLY    80      40.132   7.249   0.102  1.00  0.00              
ATOM    220  O   GLY    80      39.979   6.016  -0.027  1.00  0.00              
ATOM    221  N   GLU    81      39.146   8.055   0.548  1.00  0.00              
ATOM    222  CA  GLU    81      37.824   7.490   0.928  1.00  0.00              
ATOM    223  C   GLU    81      37.120   6.911  -0.296  1.00  0.00              
ATOM    224  O   GLU    81      36.583   5.806  -0.280  1.00  0.00              
ATOM    225  N   TRP    82      37.196   7.683  -1.372  1.00  0.00              
ATOM    226  CA  TRP    82      36.617   7.325  -2.642  1.00  0.00              
ATOM    227  C   TRP    82      37.207   6.025  -3.180  1.00  0.00              
ATOM    228  O   TRP    82      36.513   5.165  -3.729  1.00  0.00              
ATOM    229  N   ASP    83      38.510   5.897  -3.079  1.00  0.00              
ATOM    230  CA  ASP    83      39.175   4.693  -3.565  1.00  0.00              
ATOM    231  C   ASP    83      38.730   3.499  -2.760  1.00  0.00              
ATOM    232  O   ASP    83      38.616   2.429  -3.334  1.00  0.00              
ATOM    233  N   LYS    84      38.519   3.703  -1.443  1.00  0.00              
ATOM    234  CA  LYS    84      38.055   2.653  -0.579  1.00  0.00              
ATOM    235  C   LYS    84      36.644   2.165  -1.042  1.00  0.00              
ATOM    236  O   LYS    84      36.331   0.965  -1.050  1.00  0.00              
ATOM    237  N   ILE    85      35.774   3.115  -1.442  1.00  0.00              
ATOM    238  CA  ILE    85      34.450   2.772  -1.917  1.00  0.00              
ATOM    239  C   ILE    85      34.523   2.054  -3.264  1.00  0.00              
ATOM    240  O   ILE    85      33.802   1.086  -3.519  1.00  0.00              
ATOM    241  N   LYS    86      35.381   2.550  -4.159  1.00  0.00              
ATOM    242  CA  LYS    86      35.560   1.959  -5.492  1.00  0.00              
ATOM    243  C   LYS    86      36.055   0.504  -5.479  1.00  0.00              
ATOM    244  O   LYS    86      35.539  -0.355  -6.198  1.00  0.00              
ATOM    245  N   LYS    87      37.067   0.241  -4.641  1.00  0.00              
ATOM    246  CA  LYS    87      37.730  -1.034  -4.574  1.00  0.00              
ATOM    247  C   LYS    87      37.294  -1.965  -3.490  1.00  0.00              
ATOM    248  O   LYS    87      37.458  -3.159  -3.622  1.00  0.00              
END
