REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0056AL009_3 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0056  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0056, DnaB helicase N-terminal domain  
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 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 3bct 
ATOM      1  N   ILE    30      52.592  91.033  46.762  1.00  0.00              
ATOM      2  CA  ILE    30      53.215  91.482  45.520  1.00  0.00              
ATOM      3  C   ILE    30      54.612  90.908  45.237  1.00  0.00              
ATOM      4  O   ILE    30      54.902  90.497  44.116  1.00  0.00              
ATOM      5  N   GLU    31      55.482  90.857  46.236  1.00  0.00              
ATOM      6  CA  GLU    31      56.809  90.308  45.980  1.00  0.00              
ATOM      7  C   GLU    31      56.699  88.812  45.664  1.00  0.00              
ATOM      8  O   GLU    31      57.443  88.285  44.834  1.00  0.00              
ATOM      9  N   ALA    32      55.759  88.127  46.304  1.00  0.00              
ATOM     10  CA  ALA    32      55.604  86.715  46.008  1.00  0.00              
ATOM     11  C   ALA    32      55.134  86.535  44.566  1.00  0.00              
ATOM     12  O   ALA    32      55.533  85.570  43.907  1.00  0.00              
ATOM     13  N   GLU    33      54.297  87.452  44.073  1.00  0.00              
ATOM     14  CA  GLU    33      53.809  87.362  42.682  1.00  0.00              
ATOM     15  C   GLU    33      54.973  87.500  41.707  1.00  0.00              
ATOM     16  O   GLU    33      54.996  86.866  40.650  1.00  0.00              
ATOM     17  N   GLN    34      55.944  88.327  42.063  1.00  0.00              
ATOM     18  CA  GLN    34      57.109  88.506  41.209  1.00  0.00              
ATOM     19  C   GLN    34      57.900  87.209  41.150  1.00  0.00              
ATOM     20  O   GLN    34      58.300  86.775  40.077  1.00  0.00              
ATOM     21  N   SER    35      58.118  86.586  42.303  1.00  0.00              
ATOM     22  CA  SER    35      58.861  85.322  42.346  1.00  0.00              
ATOM     23  C   SER    35      58.120  84.214  41.592  1.00  0.00              
ATOM     24  O   SER    35      58.699  83.521  40.749  1.00  0.00              
ATOM     25  N   VAL    36      56.837  84.047  41.903  1.00  0.00              
ATOM     26  CA  VAL    36      56.012  83.036  41.259  1.00  0.00              
ATOM     27  C   VAL    36      56.059  83.141  39.730  1.00  0.00              
ATOM     28  O   VAL    36      56.224  82.133  39.024  1.00  0.00              
ATOM     29  N   LEU    37      55.918  84.370  39.239  1.00  0.00              
ATOM     30  CA  LEU    37      55.960  84.674  37.817  1.00  0.00              
ATOM     31  C   LEU    37      57.363  84.414  37.256  1.00  0.00              
ATOM     32  O   LEU    37      57.506  83.863  36.166  1.00  0.00              
ATOM     33  N   GLY    38      58.395  84.836  37.986  1.00  0.00              
ATOM     34  CA  GLY    38      59.755  84.635  37.512  1.00  0.00              
ATOM     35  C   GLY    38      60.114  83.169  37.318  1.00  0.00              
ATOM     36  O   GLY    38      61.074  82.857  36.633  1.00  0.00              
ATOM     37  N   TRP    47      53.135  80.480  34.891  1.00  0.00              
ATOM     38  CA  TRP    47      51.933  80.818  34.135  1.00  0.00              
ATOM     39  C   TRP    47      51.530  79.794  33.082  1.00  0.00              
ATOM     40  O   TRP    47      50.354  79.421  32.996  1.00  0.00              
ATOM     41  N   ASP    48      52.481  79.313  32.267  1.00  0.00              
ATOM     42  CA  ASP    48      52.063  78.325  31.268  1.00  0.00              
ATOM     43  C   ASP    48      51.412  77.122  31.932  1.00  0.00              
ATOM     44  O   ASP    48      50.400  76.603  31.453  1.00  0.00              
ATOM     45  N   ASP    49      51.994  76.688  33.047  1.00  0.00              
ATOM     46  CA  ASP    49      51.463  75.543  33.774  1.00  0.00              
ATOM     47  C   ASP    49      50.100  75.851  34.416  1.00  0.00              
ATOM     48  O   ASP    49      49.173  75.061  34.302  1.00  0.00              
ATOM     49  N   VAL    50      49.970  76.999  35.077  1.00  0.00              
ATOM     50  CA  VAL    50      48.701  77.335  35.709  1.00  0.00              
ATOM     51  C   VAL    50      47.591  77.319  34.678  1.00  0.00              
ATOM     52  O   VAL    50      46.495  76.830  34.946  1.00  0.00              
ATOM     53  N   ALA    51      47.875  77.867  33.498  1.00  0.00              
ATOM     54  CA  ALA    51      46.894  77.902  32.428  1.00  0.00              
ATOM     55  C   ALA    51      46.538  76.482  31.973  1.00  0.00              
ATOM     56  O   ALA    51      45.372  76.166  31.722  1.00  0.00              
ATOM     57  N   GLU    52      47.539  75.620  31.875  1.00  0.00              
ATOM     58  CA  GLU    52      47.284  74.249  31.469  1.00  0.00              
ATOM     59  C   GLU    52      46.382  73.540  32.492  1.00  0.00              
ATOM     60  O   GLU    52      45.562  72.687  32.128  1.00  0.00              
ATOM     61  N   THR    61      37.790  69.547  39.573  1.00  0.00              
ATOM     62  CA  THR    61      37.310  70.888  39.856  1.00  0.00              
ATOM     63  C   THR    61      38.154  71.678  40.843  1.00  0.00              
ATOM     64  O   THR    61      38.408  72.862  40.632  1.00  0.00              
ATOM     65  N   ARG    62      38.581  71.040  41.925  1.00  0.00              
ATOM     66  CA  ARG    62      39.389  71.750  42.900  1.00  0.00              
ATOM     67  C   ARG    62      40.699  72.252  42.303  1.00  0.00              
ATOM     68  O   ARG    62      41.198  73.303  42.709  1.00  0.00              
ATOM     69  N   PRO    63      41.253  71.526  41.337  1.00  0.00              
ATOM     70  CA  PRO    63      42.487  71.982  40.706  1.00  0.00              
ATOM     71  C   PRO    63      42.138  73.158  39.800  1.00  0.00              
ATOM     72  O   PRO    63      42.883  74.130  39.709  1.00  0.00              
ATOM     73  N   HIS    64      40.986  73.069  39.142  1.00  0.00              
ATOM     74  CA  HIS    64      40.531  74.149  38.276  1.00  0.00              
ATOM     75  C   HIS    64      40.368  75.379  39.137  1.00  0.00              
ATOM     76  O   HIS    64      40.659  76.498  38.714  1.00  0.00              
ATOM     77  N   ARG    65      39.897  75.168  40.359  1.00  0.00              
ATOM     78  CA  ARG    65      39.653  76.290  41.244  1.00  0.00              
ATOM     79  C   ARG    65      40.903  77.021  41.710  1.00  0.00              
ATOM     80  O   ARG    65      40.964  78.248  41.628  1.00  0.00              
ATOM     81  N   HIS    66      41.893  76.294  42.220  1.00  0.00              
ATOM     82  CA  HIS    66      43.092  76.979  42.691  1.00  0.00              
ATOM     83  C   HIS    66      43.931  77.528  41.531  1.00  0.00              
ATOM     84  O   HIS    66      44.637  78.525  41.684  1.00  0.00              
ATOM     85  N   ILE    67      43.839  76.899  40.363  1.00  0.00              
ATOM     86  CA  ILE    67      44.594  77.383  39.207  1.00  0.00              
ATOM     87  C   ILE    67      43.997  78.724  38.771  1.00  0.00              
ATOM     88  O   ILE    67      44.720  79.695  38.538  1.00  0.00              
ATOM     89  N   PHE    68      42.670  78.786  38.688  1.00  0.00              
ATOM     90  CA  PHE    68      42.013  80.020  38.298  1.00  0.00              
ATOM     91  C   PHE    68      42.227  81.070  39.385  1.00  0.00              
ATOM     92  O   PHE    68      42.332  82.259  39.109  1.00  0.00              
ATOM     93  N   THR    69      42.278  80.631  40.632  1.00  0.00              
ATOM     94  CA  THR    69      42.488  81.569  41.717  1.00  0.00              
ATOM     95  C   THR    69      43.890  82.174  41.717  1.00  0.00              
ATOM     96  O   THR    69      44.037  83.391  41.935  1.00  0.00              
ATOM     97  N   GLU    70      44.929  81.356  41.482  1.00  0.00              
ATOM     98  CA  GLU    70      46.276  81.918  41.474  1.00  0.00              
ATOM     99  C   GLU    70      46.446  82.830  40.252  1.00  0.00              
ATOM    100  O   GLU    70      47.131  83.861  40.325  1.00  0.00              
ATOM    101  N   MET    71      45.832  82.457  39.129  1.00  0.00              
ATOM    102  CA  MET    71      45.906  83.302  37.940  1.00  0.00              
ATOM    103  C   MET    71      45.205  84.617  38.285  1.00  0.00              
ATOM    104  O   MET    71      45.693  85.706  37.972  1.00  0.00              
ATOM    105  N   ALA    72      44.075  84.516  38.973  1.00  0.00              
ATOM    106  CA  ALA    72      43.343  85.711  39.348  1.00  0.00              
ATOM    107  C   ALA    72      44.213  86.665  40.157  1.00  0.00              
ATOM    108  O   ALA    72      44.223  87.868  39.886  1.00  0.00              
ATOM    109  N   ARG    73      44.943  86.148  41.150  1.00  0.00              
ATOM    110  CA  ARG    73      45.833  87.011  41.938  1.00  0.00              
ATOM    111  C   ARG    73      46.910  87.625  41.037  1.00  0.00              
ATOM    112  O   ARG    73      47.217  88.810  41.134  1.00  0.00              
ATOM    113  N   LEU    74      47.504  86.804  40.180  1.00  0.00              
ATOM    114  CA  LEU    74      48.577  87.285  39.317  1.00  0.00              
ATOM    115  C   LEU    74      48.127  88.362  38.351  1.00  0.00              
ATOM    116  O   LEU    74      48.844  89.330  38.126  1.00  0.00              
ATOM    117  N   ILE    84      49.289  94.257  35.655  1.00  0.00              
ATOM    118  CA  ILE    84      49.161  94.353  34.207  1.00  0.00              
ATOM    119  C   ILE    84      50.135  93.481  33.422  1.00  0.00              
ATOM    120  O   ILE    84      49.719  92.757  32.531  1.00  0.00              
ATOM    121  N   THR    85      51.420  93.516  33.748  1.00  0.00              
ATOM    122  CA  THR    85      52.379  92.705  32.992  1.00  0.00              
ATOM    123  C   THR    85      51.987  91.221  33.038  1.00  0.00              
ATOM    124  O   THR    85      52.112  90.502  32.034  1.00  0.00              
ATOM    125  N   LEU    86      51.507  90.777  34.201  1.00  0.00              
ATOM    126  CA  LEU    86      51.097  89.393  34.371  1.00  0.00              
ATOM    127  C   LEU    86      49.830  89.098  33.574  1.00  0.00              
ATOM    128  O   LEU    86      49.712  88.025  32.958  1.00  0.00              
ATOM    129  N   ALA    87      48.883  90.037  33.580  1.00  0.00              
ATOM    130  CA  ALA    87      47.633  89.838  32.839  1.00  0.00              
ATOM    131  C   ALA    87      47.935  89.592  31.361  1.00  0.00              
ATOM    132  O   ALA    87      47.330  88.723  30.730  1.00  0.00              
ATOM    133  N   GLU    88      48.873  90.353  30.806  1.00  0.00              
ATOM    134  CA  GLU    88      49.239  90.177  29.396  1.00  0.00              
ATOM    135  C   GLU    88      49.878  88.801  29.165  1.00  0.00              
ATOM    136  O   GLU    88      49.603  88.137  28.167  1.00  0.00              
ATOM    137  N   SER    89      50.735  88.383  30.092  1.00  0.00              
ATOM    138  CA  SER    89      51.385  87.083  29.982  1.00  0.00              
ATOM    139  C   SER    89      50.327  85.969  30.028  1.00  0.00              
ATOM    140  O   SER    89      50.375  85.015  29.254  1.00  0.00              
ATOM    141  N   LEU    90      49.363  86.100  30.932  1.00  0.00              
ATOM    142  CA  LEU    90      48.301  85.105  31.056  1.00  0.00              
ATOM    143  C   LEU    90      47.490  85.051  29.747  1.00  0.00              
ATOM    144  O   LEU    90      47.187  83.976  29.232  1.00  0.00              
ATOM    145  N   GLU    91      47.141  86.214  29.211  1.00  0.00              
ATOM    146  CA  GLU    91      46.419  86.252  27.953  1.00  0.00              
ATOM    147  C   GLU    91      47.269  85.644  26.830  1.00  0.00              
ATOM    148  O   GLU    91      46.781  84.843  26.030  1.00  0.00              
ATOM    149  N   ARG    92      48.543  86.024  26.777  1.00  0.00              
ATOM    150  CA  ARG    92      49.449  85.509  25.756  1.00  0.00              
ATOM    151  C   ARG    92      49.529  83.991  25.826  1.00  0.00              
ATOM    152  O   ARG    92      49.927  83.335  24.861  1.00  0.00              
ATOM    153  N   PHE   102      42.284  82.765  27.761  1.00  0.00              
ATOM    154  CA  PHE   102      40.936  83.262  27.526  1.00  0.00              
ATOM    155  C   PHE   102      39.944  82.157  27.191  1.00  0.00              
ATOM    156  O   PHE   102      38.858  82.110  27.754  1.00  0.00              
ATOM    157  N   ALA   103      40.326  81.264  26.285  1.00  0.00              
ATOM    158  CA  ALA   103      39.455  80.173  25.882  1.00  0.00              
ATOM    159  C   ALA   103      39.079  79.280  27.062  1.00  0.00              
ATOM    160  O   ALA   103      37.903  79.192  27.428  1.00  0.00              
ATOM    161  N   TYR   104      40.065  78.611  27.685  1.00  0.00              
ATOM    162  CA  TYR   104      39.712  77.750  28.815  1.00  0.00              
ATOM    163  C   TYR   104      38.952  78.489  29.918  1.00  0.00              
ATOM    164  O   TYR   104      37.999  77.948  30.479  1.00  0.00              
ATOM    165  N   LEU   105      39.358  79.720  30.227  1.00  0.00              
ATOM    166  CA  LEU   105      38.674  80.497  31.262  1.00  0.00              
ATOM    167  C   LEU   105      37.195  80.692  30.911  1.00  0.00              
ATOM    168  O   LEU   105      36.317  80.539  31.755  1.00  0.00              
ATOM    169  N   ALA   106      36.939  81.042  29.653  1.00  0.00              
ATOM    170  CA  ALA   106      35.588  81.269  29.157  1.00  0.00              
ATOM    171  C   ALA   106      34.716  80.051  29.397  1.00  0.00              
ATOM    172  O   ALA   106      33.606  80.165  29.912  1.00  0.00              
ATOM    173  N   GLU   107      35.217  78.885  29.019  1.00  0.00              
ATOM    174  CA  GLU   107      34.457  77.662  29.218  1.00  0.00              
ATOM    175  C   GLU   107      34.117  77.537  30.702  1.00  0.00              
ATOM    176  O   GLU   107      32.946  77.436  31.072  1.00  0.00              
ATOM    177  N   LEU   108      35.151  77.562  31.544  1.00  0.00              
ATOM    178  CA  LEU   108      34.985  77.449  32.991  1.00  0.00              
ATOM    179  C   LEU   108      33.982  78.427  33.574  1.00  0.00              
ATOM    180  O   LEU   108      33.583  78.284  34.726  1.00  0.00              
ATOM    181  N   ALA   116      30.804  76.752  41.502  1.00  0.00              
ATOM    182  CA  ALA   116      30.731  78.201  41.597  1.00  0.00              
ATOM    183  C   ALA   116      32.059  78.933  41.843  1.00  0.00              
ATOM    184  O   ALA   116      32.269  80.027  41.317  1.00  0.00              
ATOM    185  N   ASN   117      32.957  78.335  42.625  1.00  0.00              
ATOM    186  CA  ASN   117      34.247  78.965  42.888  1.00  0.00              
ATOM    187  C   ASN   117      35.064  79.063  41.612  1.00  0.00              
ATOM    188  O   ASN   117      35.679  80.087  41.315  1.00  0.00              
ATOM    189  N   ILE   118      35.083  77.972  40.860  1.00  0.00              
ATOM    190  CA  ILE   118      35.774  77.924  39.580  1.00  0.00              
ATOM    191  C   ILE   118      35.244  79.059  38.711  1.00  0.00              
ATOM    192  O   ILE   118      35.984  79.967  38.320  1.00  0.00              
ATOM    193  N   SER   119      33.944  79.008  38.432  1.00  0.00              
ATOM    194  CA  SER   119      33.278  80.012  37.599  1.00  0.00              
ATOM    195  C   SER   119      33.614  81.430  38.023  1.00  0.00              
ATOM    196  O   SER   119      33.941  82.288  37.197  1.00  0.00              
ATOM    197  N   ALA   120      33.523  81.673  39.321  1.00  0.00              
ATOM    198  CA  ALA   120      33.798  82.984  39.876  1.00  0.00              
ATOM    199  C   ALA   120      35.235  83.449  39.655  1.00  0.00              
ATOM    200  O   ALA   120      35.470  84.642  39.419  1.00  0.00              
ATOM    201  N   TYR   121      36.197  82.525  39.744  1.00  0.00              
ATOM    202  CA  TYR   121      37.596  82.891  39.518  1.00  0.00              
ATOM    203  C   TYR   121      37.869  83.111  38.036  1.00  0.00              
ATOM    204  O   TYR   121      38.641  84.000  37.666  1.00  0.00              
ATOM    205  N   ALA   122      37.249  82.296  37.191  1.00  0.00              
ATOM    206  CA  ALA   122      37.440  82.434  35.754  1.00  0.00              
ATOM    207  C   ALA   122      36.958  83.810  35.330  1.00  0.00              
ATOM    208  O   ALA   122      37.625  84.496  34.557  1.00  0.00              
ATOM    209  N   ASP   123      35.799  84.215  35.842  1.00  0.00              
ATOM    210  CA  ASP   123      35.242  85.525  35.508  1.00  0.00              
ATOM    211  C   ASP   123      36.174  86.658  35.944  1.00  0.00              
ATOM    212  O   ASP   123      36.360  87.626  35.223  1.00  0.00              
ATOM    213  N   ILE   124      36.758  86.545  37.131  1.00  0.00              
ATOM    214  CA  ILE   124      37.647  87.600  37.602  1.00  0.00              
ATOM    215  C   ILE   124      38.919  87.706  36.755  1.00  0.00              
ATOM    216  O   ILE   124      39.433  88.806  36.544  1.00  0.00              
ATOM    217  N   VAL   125      39.428  86.575  36.264  1.00  0.00              
ATOM    218  CA  VAL   125      40.646  86.619  35.463  1.00  0.00              
ATOM    219  C   VAL   125      40.308  87.298  34.141  1.00  0.00              
ATOM    220  O   VAL   125      41.039  88.173  33.689  1.00  0.00              
ATOM    221  N   ARG   126      39.193  86.886  33.530  1.00  0.00              
ATOM    222  CA  ARG   126      38.722  87.470  32.267  1.00  0.00              
ATOM    223  C   ARG   126      38.569  88.975  32.378  1.00  0.00              
ATOM    224  O   ARG   126      38.921  89.711  31.458  1.00  0.00              
ATOM    225  N   GLU   127      38.031  89.426  33.506  1.00  0.00              
ATOM    226  CA  GLU   127      37.835  90.845  33.725  1.00  0.00              
ATOM    227  C   GLU   127      39.161  91.583  33.736  1.00  0.00              
ATOM    228  O   GLU   127      39.342  92.558  33.002  1.00  0.00              
END
