REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0061AL009_5 
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  5   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 3bct 
ATOM      1  N   ALA     3      48.357  80.998  63.359  1.00  0.00              
ATOM      2  CA  ALA     3      49.195  81.210  62.180  1.00  0.00              
ATOM      3  C   ALA     3      50.455  81.996  62.532  1.00  0.00              
ATOM      4  O   ALA     3      51.547  81.687  62.035  1.00  0.00              
ATOM      5  N   GLN     4      50.290  83.030  63.357  1.00  0.00              
ATOM      6  CA  GLN     4      51.407  83.859  63.829  1.00  0.00              
ATOM      7  C   GLN     4      52.276  83.078  64.805  1.00  0.00              
ATOM      8  O   GLN     4      53.505  83.176  64.776  1.00  0.00              
ATOM      9  N   LYS     5      51.623  82.319  65.682  1.00  0.00              
ATOM     10  CA  LYS     5      52.334  81.532  66.682  1.00  0.00              
ATOM     11  C   LYS     5      53.343  80.553  66.074  1.00  0.00              
ATOM     12  O   LYS     5      54.401  80.310  66.661  1.00  0.00              
ATOM     13  N   ALA     6      53.033  79.988  64.907  1.00  0.00              
ATOM     14  CA  ALA     6      53.975  79.059  64.290  1.00  0.00              
ATOM     15  C   ALA     6      55.273  79.805  63.998  1.00  0.00              
ATOM     16  O   ALA     6      56.372  79.284  64.223  1.00  0.00              
ATOM     17  N   ALA     7      55.134  81.034  63.512  1.00  0.00              
ATOM     18  CA  ALA     7      56.281  81.870  63.172  1.00  0.00              
ATOM     19  C   ALA     7      57.037  82.264  64.442  1.00  0.00              
ATOM     20  O   ALA     7      58.258  82.080  64.559  1.00  0.00              
ATOM     21  N   ASP     8      56.279  82.802  65.387  1.00  0.00              
ATOM     22  CA  ASP     8      56.817  83.268  66.644  1.00  0.00              
ATOM     23  C   ASP     8      57.604  82.209  67.399  1.00  0.00              
ATOM     24  O   ASP     8      58.538  82.545  68.118  1.00  0.00              
ATOM     25  N   CYS    18      58.679  78.463  60.952  1.00  0.00              
ATOM     26  CA  CYS    18      58.707  78.558  59.490  1.00  0.00              
ATOM     27  C   CYS    18      59.817  77.853  58.735  1.00  0.00              
ATOM     28  O   CYS    18      59.548  77.210  57.727  1.00  0.00              
ATOM     29  N   GLU    19      61.074  77.957  59.194  1.00  0.00              
ATOM     30  CA  GLU    19      62.183  77.293  58.490  1.00  0.00              
ATOM     31  C   GLU    19      62.063  75.762  58.412  1.00  0.00              
ATOM     32  O   GLU    19      62.300  75.167  57.360  1.00  0.00              
ATOM     33  N   ASP    20      61.693  75.132  59.520  1.00  0.00              
ATOM     34  CA  ASP    20      61.572  73.683  59.538  1.00  0.00              
ATOM     35  C   ASP    20      60.365  73.225  58.725  1.00  0.00              
ATOM     36  O   ASP    20      60.396  72.146  58.127  1.00  0.00              
ATOM     37  N   PHE    21      59.308  74.038  58.690  1.00  0.00              
ATOM     38  CA  PHE    21      58.125  73.682  57.898  1.00  0.00              
ATOM     39  C   PHE    21      58.564  73.642  56.428  1.00  0.00              
ATOM     40  O   PHE    21      58.271  72.689  55.710  1.00  0.00              
ATOM     41  N   LEU    22      59.282  74.658  55.967  1.00  0.00              
ATOM     42  CA  LEU    22      59.744  74.634  54.565  1.00  0.00              
ATOM     43  C   LEU    22      60.732  73.494  54.329  1.00  0.00              
ATOM     44  O   LEU    22      60.677  72.819  53.302  1.00  0.00              
ATOM     45  N   ALA    23      61.641  73.274  55.271  1.00  0.00              
ATOM     46  CA  ALA    23      62.604  72.190  55.096  1.00  0.00              
ATOM     47  C   ALA    23      61.925  70.847  54.864  1.00  0.00              
ATOM     48  O   ALA    23      62.436  70.035  54.108  1.00  0.00              
ATOM     49  N   GLU    26      55.964  61.294  50.681  1.00  0.00              
ATOM     50  CA  GLU    26      54.735  61.967  50.280  1.00  0.00              
ATOM     51  C   GLU    26      53.676  62.343  51.322  1.00  0.00              
ATOM     52  O   GLU    26      53.157  63.456  51.282  1.00  0.00              
ATOM     53  N   SER    27      53.353  61.444  52.272  1.00  0.00              
ATOM     54  CA  SER    27      52.330  61.838  53.248  1.00  0.00              
ATOM     55  C   SER    27      52.742  63.113  53.958  1.00  0.00              
ATOM     56  O   SER    27      51.946  64.022  54.133  1.00  0.00              
ATOM     57  N   PHE    28      54.010  63.174  54.346  1.00  0.00              
ATOM     58  CA  PHE    28      54.529  64.332  55.039  1.00  0.00              
ATOM     59  C   PHE    28      54.532  65.596  54.175  1.00  0.00              
ATOM     60  O   PHE    28      54.184  66.680  54.652  1.00  0.00              
ATOM     61  N   GLN    29      54.935  65.467  52.917  1.00  0.00              
ATOM     62  CA  GLN    29      54.978  66.616  52.028  1.00  0.00              
ATOM     63  C   GLN    29      53.558  67.151  51.804  1.00  0.00              
ATOM     64  O   GLN    29      53.327  68.364  51.814  1.00  0.00              
ATOM     65  N   PRO    30      52.608  66.242  51.627  1.00  0.00              
ATOM     66  CA  PRO    30      51.203  66.617  51.426  1.00  0.00              
ATOM     67  C   PRO    30      50.698  67.429  52.618  1.00  0.00              
ATOM     68  O   PRO    30      50.087  68.503  52.454  1.00  0.00              
ATOM     69  N   THR    31      50.969  66.930  53.821  1.00  0.00              
ATOM     70  CA  THR    31      50.550  67.639  55.026  1.00  0.00              
ATOM     71  C   THR    31      51.244  68.999  55.136  1.00  0.00              
ATOM     72  O   THR    31      50.594  70.004  55.439  1.00  0.00              
ATOM     73  N   ALA    32      52.553  69.025  54.871  1.00  0.00              
ATOM     74  CA  ALA    32      53.354  70.246  54.988  1.00  0.00              
ATOM     75  C   ALA    32      52.876  71.322  54.028  1.00  0.00              
ATOM     76  O   ALA    32      52.763  72.487  54.402  1.00  0.00              
ATOM     77  N   VAL    33      52.596  70.939  52.788  1.00  0.00              
ATOM     78  CA  VAL    33      52.072  71.889  51.825  1.00  0.00              
ATOM     79  C   VAL    33      50.768  72.473  52.403  1.00  0.00              
ATOM     80  O   VAL    33      50.547  73.692  52.382  1.00  0.00              
ATOM     81  N   GLY    34      49.911  71.596  52.927  1.00  0.00              
ATOM     82  CA  GLY    34      48.649  72.038  53.502  1.00  0.00              
ATOM     83  C   GLY    34      48.849  73.049  54.615  1.00  0.00              
ATOM     84  O   GLY    34      48.094  74.029  54.722  1.00  0.00              
ATOM     85  N   PHE    35      49.861  72.814  55.454  1.00  0.00              
ATOM     86  CA  PHE    35      50.168  73.730  56.536  1.00  0.00              
ATOM     87  C   PHE    35      50.637  75.093  56.014  1.00  0.00              
ATOM     88  O   PHE    35      50.209  76.126  56.509  1.00  0.00              
ATOM     89  N   ALA    36      51.513  75.092  55.014  1.00  0.00              
ATOM     90  CA  ALA    36      52.034  76.336  54.445  1.00  0.00              
ATOM     91  C   ALA    36      50.894  77.195  53.878  1.00  0.00              
ATOM     92  O   ALA    36      50.876  78.424  54.032  1.00  0.00              
ATOM     93  N   GLU    37      49.955  76.526  53.225  1.00  0.00              
ATOM     94  CA  GLU    37      48.768  77.148  52.650  1.00  0.00              
ATOM     95  C   GLU    37      48.046  77.947  53.736  1.00  0.00              
ATOM     96  O   GLU    37      47.650  79.101  53.517  1.00  0.00              
ATOM     97  N   ALA    38      47.886  77.339  54.912  1.00  0.00              
ATOM     98  CA  ALA    38      47.227  78.017  56.031  1.00  0.00              
ATOM     99  C   ALA    38      48.096  79.129  56.601  1.00  0.00              
ATOM    100  O   ALA    38      47.595  80.216  56.911  1.00  0.00              
ATOM    101  N   LEU    39      49.396  78.866  56.738  1.00  0.00              
ATOM    102  CA  LEU    39      50.315  79.875  57.249  1.00  0.00              
ATOM    103  C   LEU    39      50.293  81.124  56.348  1.00  0.00              
ATOM    104  O   LEU    39      50.351  82.251  56.838  1.00  0.00              
ATOM    105  N   GLU    46      53.952  86.088  54.939  1.00  0.00              
ATOM    106  CA  GLU    46      54.229  86.148  53.506  1.00  0.00              
ATOM    107  C   GLU    46      55.716  86.295  53.202  1.00  0.00              
ATOM    108  O   GLU    46      56.264  85.492  52.445  1.00  0.00              
ATOM    109  N   ASP    47      56.363  87.296  53.798  1.00  0.00              
ATOM    110  CA  ASP    47      57.786  87.543  53.572  1.00  0.00              
ATOM    111  C   ASP    47      58.663  86.433  54.132  1.00  0.00              
ATOM    112  O   ASP    47      59.546  85.926  53.439  1.00  0.00              
ATOM    113  N   ALA    48      58.480  86.086  55.415  1.00  0.00              
ATOM    114  CA  ALA    48      59.337  85.011  55.909  1.00  0.00              
ATOM    115  C   ALA    48      59.193  83.692  55.100  1.00  0.00              
ATOM    116  O   ALA    48      60.195  83.043  54.843  1.00  0.00              
ATOM    117  N   VAL    49      57.989  83.303  54.670  1.00  0.00              
ATOM    118  CA  VAL    49      57.875  82.060  53.880  1.00  0.00              
ATOM    119  C   VAL    49      58.674  82.192  52.569  1.00  0.00              
ATOM    120  O   VAL    49      59.314  81.232  52.115  1.00  0.00              
ATOM    121  N   LEU    50      58.647  83.385  51.971  1.00  0.00              
ATOM    122  CA  LEU    50      59.399  83.660  50.746  1.00  0.00              
ATOM    123  C   LEU    50      60.925  83.583  51.021  1.00  0.00              
ATOM    124  O   LEU    50      61.677  82.932  50.294  1.00  0.00              
ATOM    125  N   ASP    51      61.373  84.240  52.084  1.00  0.00              
ATOM    126  CA  ASP    51      62.797  84.261  52.429  1.00  0.00              
ATOM    127  C   ASP    51      63.291  82.860  52.767  1.00  0.00              
ATOM    128  O   ASP    51      64.427  82.517  52.465  1.00  0.00              
ATOM    129  N   VAL    58      60.100  78.907  50.365  1.00  0.00              
ATOM    130  CA  VAL    58      58.900  78.117  50.135  1.00  0.00              
ATOM    131  C   VAL    58      58.459  78.083  48.671  1.00  0.00              
ATOM    132  O   VAL    58      58.098  77.028  48.141  1.00  0.00              
ATOM    133  N   THR    59      58.524  79.224  47.995  1.00  0.00              
ATOM    134  CA  THR    59      58.043  79.276  46.627  1.00  0.00              
ATOM    135  C   THR    59      58.724  78.374  45.583  1.00  0.00              
ATOM    136  O   THR    59      58.040  77.615  44.896  1.00  0.00              
ATOM    137  N   PRO    60      60.048  78.481  45.405  1.00  0.00              
ATOM    138  CA  PRO    60      60.624  77.582  44.397  1.00  0.00              
ATOM    139  C   PRO    60      60.407  76.081  44.668  1.00  0.00              
ATOM    140  O   PRO    60      60.235  75.300  43.740  1.00  0.00              
ATOM    141  N   ALA    61      60.422  75.663  45.927  1.00  0.00              
ATOM    142  CA  ALA    61      60.227  74.239  46.214  1.00  0.00              
ATOM    143  C   ALA    61      58.766  73.847  45.935  1.00  0.00              
ATOM    144  O   ALA    61      58.497  72.762  45.406  1.00  0.00              
ATOM    145  N   ILE    62      57.823  74.714  46.306  1.00  0.00              
ATOM    146  CA  ILE    62      56.414  74.443  46.029  1.00  0.00              
ATOM    147  C   ILE    62      56.247  74.331  44.518  1.00  0.00              
ATOM    148  O   ILE    62      55.519  73.463  44.032  1.00  0.00              
ATOM    149  N   VAL    63      56.921  75.208  43.772  1.00  0.00              
ATOM    150  CA  VAL    63      56.810  75.172  42.326  1.00  0.00              
ATOM    151  C   VAL    63      57.436  73.903  41.730  1.00  0.00              
ATOM    152  O   VAL    63      56.836  73.277  40.842  1.00  0.00              
ATOM    153  N   GLN    64      58.623  73.514  42.202  1.00  0.00              
ATOM    154  CA  GLN    64      59.251  72.290  41.686  1.00  0.00              
ATOM    155  C   GLN    64      58.352  71.079  41.971  1.00  0.00              
ATOM    156  O   GLN    64      58.174  70.212  41.120  1.00  0.00              
ATOM    157  N   ALA    65      57.802  71.013  43.180  1.00  0.00              
ATOM    158  CA  ALA    65      56.908  69.917  43.536  1.00  0.00              
ATOM    159  C   ALA    65      55.714  69.877  42.574  1.00  0.00              
ATOM    160  O   ALA    65      55.360  68.812  42.052  1.00  0.00              
ATOM    161  N   CYS    66      55.101  71.043  42.341  1.00  0.00              
ATOM    162  CA  CYS    66      53.945  71.175  41.440  1.00  0.00              
ATOM    163  C   CYS    66      54.243  70.688  40.021  1.00  0.00              
ATOM    164  O   CYS    66      53.497  69.886  39.450  1.00  0.00              
ATOM    165  N   THR    67      55.330  71.198  39.451  1.00  0.00              
ATOM    166  CA  THR    67      55.748  70.847  38.099  1.00  0.00              
ATOM    167  C   THR    67      55.994  69.349  37.937  1.00  0.00              
ATOM    168  O   THR    67      55.541  68.731  36.976  1.00  0.00              
ATOM    169  N   GLN    68      56.717  68.763  38.876  1.00  0.00              
ATOM    170  CA  GLN    68      57.009  67.344  38.776  1.00  0.00              
ATOM    171  C   GLN    68      55.748  66.510  38.986  1.00  0.00              
ATOM    172  O   GLN    68      55.517  65.525  38.273  1.00  0.00              
ATOM    173  N   ASP    69      54.928  66.917  39.954  1.00  0.00              
ATOM    174  CA  ASP    69      53.688  66.214  40.252  1.00  0.00              
ATOM    175  C   ASP    69      52.728  66.253  39.067  1.00  0.00              
ATOM    176  O   ASP    69      52.062  65.263  38.777  1.00  0.00              
ATOM    177  N   LYS    70      52.649  67.395  38.387  1.00  0.00              
ATOM    178  CA  LYS    70      51.765  67.502  37.232  1.00  0.00              
ATOM    179  C   LYS    70      52.233  66.545  36.130  1.00  0.00              
ATOM    180  O   LYS    70      51.424  65.819  35.548  1.00  0.00              
ATOM    181  N   GLN    71      53.537  66.544  35.853  1.00  0.00              
ATOM    182  CA  GLN    71      54.096  65.669  34.827  1.00  0.00              
ATOM    183  C   GLN    71      53.706  64.219  35.105  1.00  0.00              
ATOM    184  O   GLN    71      53.272  63.506  34.199  1.00  0.00              
ATOM    185  N   ALA    72      53.846  63.775  36.352  1.00  0.00              
ATOM    186  CA  ALA    72      53.483  62.406  36.656  1.00  0.00              
ATOM    187  C   ALA    72      52.012  62.153  36.332  1.00  0.00              
ATOM    188  O   ALA    72      51.687  61.134  35.724  1.00  0.00              
ATOM    189  N   ASN    73      51.114  63.060  36.718  1.00  0.00              
ATOM    190  CA  ASN    73      49.695  62.839  36.415  1.00  0.00              
ATOM    191  C   ASN    73      49.464  62.713  34.913  1.00  0.00              
ATOM    192  O   ASN    73      48.529  62.049  34.488  1.00  0.00              
ATOM    193  N   ASP    76      46.738  65.171  44.237  1.00  0.00              
ATOM    194  CA  ASP    76      46.611  65.861  45.523  1.00  0.00              
ATOM    195  C   ASP    76      47.735  66.871  45.714  1.00  0.00              
ATOM    196  O   ASP    76      47.504  67.958  46.252  1.00  0.00              
ATOM    197  N   LYS    77      48.948  66.504  45.290  1.00  0.00              
ATOM    198  CA  LYS    77      50.104  67.411  45.380  1.00  0.00              
ATOM    199  C   LYS    77      49.883  68.588  44.394  1.00  0.00              
ATOM    200  O   LYS    77      50.193  69.747  44.695  1.00  0.00              
ATOM    201  N   VAL    78      49.356  68.284  43.212  1.00  0.00              
ATOM    202  CA  VAL    78      49.063  69.321  42.241  1.00  0.00              
ATOM    203  C   VAL    78      48.168  70.364  42.927  1.00  0.00              
ATOM    204  O   VAL    78      48.523  71.534  43.038  1.00  0.00              
ATOM    205  N   LYS    79      47.004  69.925  43.388  1.00  0.00              
ATOM    206  CA  LYS    79      46.050  70.816  44.043  1.00  0.00              
ATOM    207  C   LYS    79      46.662  71.548  45.244  1.00  0.00              
ATOM    208  O   LYS    79      46.458  72.770  45.430  1.00  0.00              
ATOM    209  N   GLY    80      47.386  70.785  46.063  1.00  0.00              
ATOM    210  CA  GLY    80      48.016  71.336  47.247  1.00  0.00              
ATOM    211  C   GLY    80      48.958  72.498  46.977  1.00  0.00              
ATOM    212  O   GLY    80      48.780  73.597  47.529  1.00  0.00              
ATOM    213  N   GLU    81      49.949  72.271  46.118  1.00  0.00              
ATOM    214  CA  GLU    81      50.931  73.293  45.811  1.00  0.00              
ATOM    215  C   GLU    81      50.319  74.506  45.133  1.00  0.00              
ATOM    216  O   GLU    81      50.639  75.643  45.498  1.00  0.00              
ATOM    217  N   TRP    82      49.442  74.278  44.157  1.00  0.00              
ATOM    218  CA  TRP    82      48.804  75.387  43.472  1.00  0.00              
ATOM    219  C   TRP    82      47.982  76.145  44.507  1.00  0.00              
ATOM    220  O   TRP    82      47.934  77.366  44.483  1.00  0.00              
ATOM    221  N   ASP    83      47.372  75.414  45.438  1.00  0.00              
ATOM    222  CA  ASP    83      46.566  76.060  46.463  1.00  0.00              
ATOM    223  C   ASP    83      47.414  76.948  47.358  1.00  0.00              
ATOM    224  O   ASP    83      47.020  78.075  47.697  1.00  0.00              
ATOM    225  N   LYS    84      48.582  76.445  47.752  1.00  0.00              
ATOM    226  CA  LYS    84      49.472  77.225  48.594  1.00  0.00              
ATOM    227  C   LYS    84      49.947  78.460  47.816  1.00  0.00              
ATOM    228  O   LYS    84      50.042  79.544  48.368  1.00  0.00              
ATOM    229  N   ILE    85      50.259  78.281  46.538  1.00  0.00              
ATOM    230  CA  ILE    85      50.723  79.386  45.715  1.00  0.00              
ATOM    231  C   ILE    85      49.620  80.445  45.553  1.00  0.00              
ATOM    232  O   ILE    85      49.900  81.647  45.528  1.00  0.00              
ATOM    233  N   LYS    86      48.370  79.995  45.467  1.00  0.00              
ATOM    234  CA  LYS    86      47.219  80.905  45.345  1.00  0.00              
ATOM    235  C   LYS    86      47.227  81.883  46.526  1.00  0.00              
ATOM    236  O   LYS    86      47.087  83.112  46.348  1.00  0.00              
ATOM    237  N   LYS    87      47.384  81.342  47.735  1.00  0.00              
ATOM    238  CA  LYS    87      47.409  82.177  48.932  1.00  0.00              
ATOM    239  C   LYS    87      48.671  83.055  48.973  1.00  0.00              
ATOM    240  O   LYS    87      48.588  84.262  49.223  1.00  0.00              
ATOM    241  N   ASP    88      49.839  82.475  48.709  1.00  0.00              
ATOM    242  CA  ASP    88      51.065  83.273  48.751  1.00  0.00              
ATOM    243  C   ASP    88      51.022  84.446  47.770  1.00  0.00              
ATOM    244  O   ASP    88      51.579  85.520  48.043  1.00  0.00              
END
