REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0056AL009_5 
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  5   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 4cpv 
ATOM      1  N   SER    29      12.802  41.927  13.511  1.00  0.00              
ATOM      2  CA  SER    29      11.496  41.956  12.826  1.00  0.00              
ATOM      3  C   SER    29      11.652  41.819  11.327  1.00  0.00              
ATOM      4  O   SER    29      10.916  41.018  10.696  1.00  0.00              
ATOM      5  N   ILE    30      12.556  42.561  10.745  1.00  0.00              
ATOM      6  CA  ILE    30      12.825  42.573   9.313  1.00  0.00              
ATOM      7  C   ILE    30      13.331  41.240   8.775  1.00  0.00              
ATOM      8  O   ILE    30      12.974  40.887   7.628  1.00  0.00              
ATOM      9  N   GLU    31      14.119  40.560   9.547  1.00  0.00              
ATOM     10  CA  GLU    31      14.708  39.248   9.221  1.00  0.00              
ATOM     11  C   GLU    31      13.591  38.198   9.168  1.00  0.00              
ATOM     12  O   GLU    31      13.521  37.407   8.203  1.00  0.00              
ATOM     13  N   ALA    32      12.756  38.249  10.168  1.00  0.00              
ATOM     14  CA  ALA    32      11.631  37.301  10.220  1.00  0.00              
ATOM     15  C   ALA    32      10.701  37.553   9.040  1.00  0.00              
ATOM     16  O   ALA    32      10.279  36.592   8.378  1.00  0.00              
ATOM     17  N   GLU    33      10.404  38.834   8.767  1.00  0.00              
ATOM     18  CA  GLU    33       9.513  39.149   7.662  1.00  0.00              
ATOM     19  C   GLU    33      10.073  38.655   6.320  1.00  0.00              
ATOM     20  O   GLU    33       9.295  38.102   5.496  1.00  0.00              
ATOM     21  N   GLN    34      11.350  38.863   6.111  1.00  0.00              
ATOM     22  CA  GLN    34      11.982  38.447   4.845  1.00  0.00              
ATOM     23  C   GLN    34      11.949  36.930   4.734  1.00  0.00              
ATOM     24  O   GLN    34      11.660  36.393   3.641  1.00  0.00              
ATOM     25  N   SER    35      12.248  36.295   5.864  1.00  0.00              
ATOM     26  CA  SER    35      12.257  34.809   5.885  1.00  0.00              
ATOM     27  C   SER    35      10.921  34.221   5.502  1.00  0.00              
ATOM     28  O   SER    35      10.830  33.254   4.751  1.00  0.00              
ATOM     29  N   VAL    36       9.850  34.743   6.032  1.00  0.00              
ATOM     30  CA  VAL    36       8.485  34.354   5.826  1.00  0.00              
ATOM     31  C   VAL    36       8.016  34.632   4.385  1.00  0.00              
ATOM     32  O   VAL    36       7.330  33.824   3.760  1.00  0.00              
ATOM     33  N   LEU    37       8.420  35.802   3.875  1.00  0.00              
ATOM     34  CA  LEU    37       8.032  36.148   2.485  1.00  0.00              
ATOM     35  C   LEU    37       8.632  35.142   1.498  1.00  0.00              
ATOM     36  O   LEU    37       7.944  34.680   0.566  1.00  0.00              
ATOM     37  N   GLY    38       9.861  34.735   1.700  1.00  0.00              
ATOM     38  CA  GLY    38      10.527  33.807   0.791  1.00  0.00              
ATOM     39  C   GLY    38       9.879  32.455   0.706  1.00  0.00              
ATOM     40  O   GLY    38       9.933  31.802  -0.371  1.00  0.00              
ATOM     41  N   TRP    47      14.711  24.657   5.300  1.00  0.00              
ATOM     42  CA  TRP    47      15.162  25.041   6.687  1.00  0.00              
ATOM     43  C   TRP    47      16.456  25.770   6.732  1.00  0.00              
ATOM     44  O   TRP    47      16.597  26.701   7.565  1.00  0.00              
ATOM     45  N   ASP    48      17.447  25.398   5.892  1.00  0.00              
ATOM     46  CA  ASP    48      18.729  26.107   5.892  1.00  0.00              
ATOM     47  C   ASP    48      18.537  27.562   5.462  1.00  0.00              
ATOM     48  O   ASP    48      19.113  28.512   6.043  1.00  0.00              
ATOM     49  N   ASP    49      17.735  27.822   4.437  1.00  0.00              
ATOM     50  CA  ASP    49      17.481  29.171   3.969  1.00  0.00              
ATOM     51  C   ASP    49      16.790  29.975   5.087  1.00  0.00              
ATOM     52  O   ASP    49      17.166  31.111   5.242  1.00  0.00              
ATOM     53  N   VAL    50      15.836  29.332   5.740  1.00  0.00              
ATOM     54  CA  VAL    50      15.094  30.050   6.814  1.00  0.00              
ATOM     55  C   VAL    50      15.996  30.427   7.960  1.00  0.00              
ATOM     56  O   VAL    50      16.004  31.599   8.357  1.00  0.00              
ATOM     57  N   ALA    51      16.695  29.437   8.490  1.00  0.00              
ATOM     58  CA  ALA    51      17.612  29.696   9.652  1.00  0.00              
ATOM     59  C   ALA    51      18.625  30.771   9.372  1.00  0.00              
ATOM     60  O   ALA    51      18.905  31.630  10.235  1.00  0.00              
ATOM     61  N   GLU    52      19.198  30.720   8.170  1.00  0.00              
ATOM     62  CA  GLU    52      20.224  31.727   7.747  1.00  0.00              
ATOM     63  C   GLU    52      19.570  33.084   7.662  1.00  0.00              
ATOM     64  O   GLU    52      20.068  34.060   8.296  1.00  0.00              
ATOM     65  N   ARG    53      18.451  33.246   6.991  1.00  0.00              
ATOM     66  CA  ARG    53      17.776  34.504   6.858  1.00  0.00              
ATOM     67  C   ARG    53      17.252  35.124   8.163  1.00  0.00              
ATOM     68  O   ARG    53      17.455  36.339   8.348  1.00  0.00              
ATOM     69  N   VAL    54      16.619  34.291   8.969  1.00  0.00              
ATOM     70  CA  VAL    54      16.045  34.768  10.240  1.00  0.00              
ATOM     71  C   VAL    54      17.124  35.153  11.239  1.00  0.00              
ATOM     72  O   VAL    54      16.762  35.874  12.212  1.00  0.00              
ATOM     73  N   HIS    64      24.795  28.548  21.206  1.00  0.00              
ATOM     74  CA  HIS    64      24.159  27.259  21.559  1.00  0.00              
ATOM     75  C   HIS    64      23.048  27.494  22.572  1.00  0.00              
ATOM     76  O   HIS    64      22.016  26.804  22.512  1.00  0.00              
ATOM     77  N   ARG    65      23.245  28.453  23.449  1.00  0.00              
ATOM     78  CA  ARG    65      22.347  28.907  24.495  1.00  0.00              
ATOM     79  C   ARG    65      21.011  29.453  23.970  1.00  0.00              
ATOM     80  O   ARG    65      19.930  29.095  24.408  1.00  0.00              
ATOM     81  N   HIS    66      21.176  30.386  23.028  1.00  0.00              
ATOM     82  CA  HIS    66      19.995  31.015  22.397  1.00  0.00              
ATOM     83  C   HIS    66      19.313  29.965  21.498  1.00  0.00              
ATOM     84  O   HIS    66      18.106  30.044  21.327  1.00  0.00              
ATOM     85  N   ILE    67      20.109  29.044  20.982  1.00  0.00              
ATOM     86  CA  ILE    67      19.542  27.982  20.109  1.00  0.00              
ATOM     87  C   ILE    67      18.624  27.108  20.995  1.00  0.00              
ATOM     88  O   ILE    67      17.552  26.741  20.588  1.00  0.00              
ATOM     89  N   PHE    68      19.104  26.810  22.225  1.00  0.00              
ATOM     90  CA  PHE    68      18.294  26.038  23.183  1.00  0.00              
ATOM     91  C   PHE    68      17.017  26.749  23.594  1.00  0.00              
ATOM     92  O   PHE    68      15.960  26.116  23.857  1.00  0.00              
ATOM     93  N   THR    69      17.066  28.076  23.687  1.00  0.00              
ATOM     94  CA  THR    69      15.914  28.910  24.011  1.00  0.00              
ATOM     95  C   THR    69      14.870  28.806  22.869  1.00  0.00              
ATOM     96  O   THR    69      13.680  28.662  23.035  1.00  0.00              
ATOM     97  N   GLU    70      15.378  28.885  21.627  1.00  0.00              
ATOM     98  CA  GLU    70      14.554  28.752  20.422  1.00  0.00              
ATOM     99  C   GLU    70      13.872  27.375  20.397  1.00  0.00              
ATOM    100  O   GLU    70      12.724  27.268  20.092  1.00  0.00              
ATOM    101  N   MET    71      14.645  26.339  20.743  1.00  0.00              
ATOM    102  CA  MET    71      14.140  24.967  20.775  1.00  0.00              
ATOM    103  C   MET    71      12.894  24.852  21.664  1.00  0.00              
ATOM    104  O   MET    71      11.872  24.310  21.366  1.00  0.00              
ATOM    105  N   ALA    72      13.120  25.439  22.886  1.00  0.00              
ATOM    106  CA  ALA    72      12.044  25.417  23.892  1.00  0.00              
ATOM    107  C   ALA    72      10.791  26.064  23.430  1.00  0.00              
ATOM    108  O   ALA    72       9.687  25.615  23.769  1.00  0.00              
ATOM    109  N   ARG    73      10.865  27.135  22.635  1.00  0.00              
ATOM    110  CA  ARG    73       9.718  27.822  22.078  1.00  0.00              
ATOM    111  C   ARG    73       8.983  26.898  21.064  1.00  0.00              
ATOM    112  O   ARG    73       7.762  26.760  21.086  1.00  0.00              
ATOM    113  N   LEU    74       9.795  26.245  20.218  1.00  0.00              
ATOM    114  CA  LEU    74       9.205  25.367  19.178  1.00  0.00              
ATOM    115  C   LEU    74       8.570  24.122  19.783  1.00  0.00              
ATOM    116  O   LEU    74       7.600  23.573  19.277  1.00  0.00              
ATOM    117  N   ALA    87       6.120  15.688  15.385  1.00  0.00              
ATOM    118  CA  ALA    87       5.669  16.132  14.022  1.00  0.00              
ATOM    119  C   ALA    87       4.612  17.159  14.052  1.00  0.00              
ATOM    120  O   ALA    87       4.763  18.110  13.124  1.00  0.00              
ATOM    121  N   GLU    88       3.562  17.198  14.889  1.00  0.00              
ATOM    122  CA  GLU    88       2.583  18.274  14.780  1.00  0.00              
ATOM    123  C   GLU    88       3.262  19.608  15.158  1.00  0.00              
ATOM    124  O   GLU    88       2.752  20.622  14.655  1.00  0.00              
ATOM    125  N   SER    89       4.254  19.578  16.066  1.00  0.00              
ATOM    126  CA  SER    89       4.899  20.845  16.387  1.00  0.00              
ATOM    127  C   SER    89       5.716  21.404  15.237  1.00  0.00              
ATOM    128  O   SER    89       5.747  22.619  15.000  1.00  0.00              
ATOM    129  N   LEU    90       6.341  20.518  14.497  1.00  0.00              
ATOM    130  CA  LEU    90       7.169  20.869  13.344  1.00  0.00              
ATOM    131  C   LEU    90       6.277  21.479  12.252  1.00  0.00              
ATOM    132  O   LEU    90       6.735  22.435  11.589  1.00  0.00              
ATOM    133  N   GLU    91       5.138  20.912  12.130  1.00  0.00              
ATOM    134  CA  GLU    91       4.174  21.400  11.091  1.00  0.00              
ATOM    135  C   GLU    91       3.806  22.836  11.299  1.00  0.00              
ATOM    136  O   GLU    91       3.559  23.664  10.392  1.00  0.00              
ATOM    137  N   VAL    99       2.645  18.633   4.400  1.00  0.00              
ATOM    138  CA  VAL    99       3.087  17.280   4.880  1.00  0.00              
ATOM    139  C   VAL    99       4.451  17.003   4.298  1.00  0.00              
ATOM    140  O   VAL    99       5.371  16.559   4.958  1.00  0.00              
ATOM    141  N   GLY   100       4.656  17.279   3.008  1.00  0.00              
ATOM    142  CA  GLY   100       5.910  17.096   2.320  1.00  0.00              
ATOM    143  C   GLY   100       7.044  17.889   3.010  1.00  0.00              
ATOM    144  O   GLY   100       8.143  17.372   3.202  1.00  0.00              
ATOM    145  N   GLY   101       6.744  19.138   3.318  1.00  0.00              
ATOM    146  CA  GLY   101       7.737  19.991   3.953  1.00  0.00              
ATOM    147  C   GLY   101       8.147  19.497   5.366  1.00  0.00              
ATOM    148  O   GLY   101       9.337  19.539   5.671  1.00  0.00              
ATOM    149  N   PHE   102       7.094  19.083   6.048  1.00  0.00              
ATOM    150  CA  PHE   102       7.320  18.594   7.446  1.00  0.00              
ATOM    151  C   PHE   102       8.186  17.345   7.468  1.00  0.00              
ATOM    152  O   PHE   102       9.152  17.235   8.222  1.00  0.00              
ATOM    153  N   ALA   103       7.798  16.418   6.549  1.00  0.00              
ATOM    154  CA  ALA   103       8.533  15.160   6.451  1.00  0.00              
ATOM    155  C   ALA   103       9.977  15.393   6.080  1.00  0.00              
ATOM    156  O   ALA   103      10.894  14.766   6.606  1.00  0.00              
ATOM    157  N   TYR   104      10.249  16.290   5.109  1.00  0.00              
ATOM    158  CA  TYR   104      11.578  16.611   4.681  1.00  0.00              
ATOM    159  C   TYR   104      12.426  17.195   5.826  1.00  0.00              
ATOM    160  O   TYR   104      13.569  16.860   6.004  1.00  0.00              
ATOM    161  N   LEU   105      11.801  18.087   6.573  1.00  0.00              
ATOM    162  CA  LEU   105      12.398  18.792   7.723  1.00  0.00              
ATOM    163  C   LEU   105      12.679  17.741   8.826  1.00  0.00              
ATOM    164  O   LEU   105      13.797  17.766   9.348  1.00  0.00              
ATOM    165  N   ALA   106      11.683  16.937   9.051  1.00  0.00              
ATOM    166  CA  ALA   106      11.852  15.866  10.065  1.00  0.00              
ATOM    167  C   ALA   106      13.023  15.003   9.665  1.00  0.00              
ATOM    168  O   ALA   106      13.972  14.765  10.442  1.00  0.00              
ATOM    169  N   GLU   107      13.002  14.501   8.437  1.00  0.00              
ATOM    170  CA  GLU   107      14.114  13.613   7.944  1.00  0.00              
ATOM    171  C   GLU   107      15.494  14.184   8.049  1.00  0.00              
ATOM    172  O   GLU   107      16.475  13.493   8.411  1.00  0.00              
ATOM    173  N   LEU   108      15.660  15.468   7.777  1.00  0.00              
ATOM    174  CA  LEU   108      16.938  16.165   7.848  1.00  0.00              
ATOM    175  C   LEU   108      17.489  16.263   9.292  1.00  0.00              
ATOM    176  O   LEU   108      18.678  16.203   9.484  1.00  0.00              
ATOM    177  N   SER   109      16.546  16.486  10.236  1.00  0.00              
ATOM    178  CA  SER   109      16.958  16.632  11.617  1.00  0.00              
ATOM    179  C   SER   109      16.926  15.404  12.476  1.00  0.00              
ATOM    180  O   SER   109      17.733  15.388  13.419  1.00  0.00              
ATOM    181  N   ILE   118      16.908  18.326  21.485  1.00  0.00              
ATOM    182  CA  ILE   118      17.704  19.505  21.466  1.00  0.00              
ATOM    183  C   ILE   118      19.022  19.356  20.664  1.00  0.00              
ATOM    184  O   ILE   118      19.321  20.363  20.020  1.00  0.00              
ATOM    185  N   SER   119      19.683  18.247  20.805  1.00  0.00              
ATOM    186  CA  SER   119      20.995  18.104  20.082  1.00  0.00              
ATOM    187  C   SER   119      20.714  18.025  18.575  1.00  0.00              
ATOM    188  O   SER   119      21.503  18.687  17.897  1.00  0.00              
ATOM    189  N   ALA   120      19.664  17.291  18.245  1.00  0.00              
ATOM    190  CA  ALA   120      19.372  17.228  16.766  1.00  0.00              
ATOM    191  C   ALA   120      19.021  18.577  16.265  1.00  0.00              
ATOM    192  O   ALA   120      19.418  18.983  15.155  1.00  0.00              
ATOM    193  N   TYR   121      18.267  19.350  17.038  1.00  0.00              
ATOM    194  CA  TYR   121      17.880  20.715  16.626  1.00  0.00              
ATOM    195  C   TYR   121      19.087  21.609  16.465  1.00  0.00              
ATOM    196  O   TYR   121      19.207  22.447  15.540  1.00  0.00              
ATOM    197  N   ALA   122      20.023  21.553  17.430  1.00  0.00              
ATOM    198  CA  ALA   122      21.218  22.370  17.402  1.00  0.00              
ATOM    199  C   ALA   122      22.060  22.119  16.134  1.00  0.00              
ATOM    200  O   ALA   122      22.487  23.098  15.568  1.00  0.00              
ATOM    201  N   ASP   123      22.224  20.897  15.777  1.00  0.00              
ATOM    202  CA  ASP   123      23.003  20.495  14.550  1.00  0.00              
ATOM    203  C   ASP   123      22.304  20.985  13.294  1.00  0.00              
ATOM    204  O   ASP   123      22.886  21.441  12.262  1.00  0.00              
ATOM    205  N   ILE   124      20.967  20.938  13.308  1.00  0.00              
ATOM    206  CA  ILE   124      20.125  21.383  12.191  1.00  0.00              
ATOM    207  C   ILE   124      20.281  22.863  11.948  1.00  0.00              
ATOM    208  O   ILE   124      20.299  23.368  10.788  1.00  0.00              
ATOM    209  N   VAL   125      20.408  23.653  13.024  1.00  0.00              
ATOM    210  CA  VAL   125      20.559  25.083  12.949  1.00  0.00              
ATOM    211  C   VAL   125      21.941  25.588  12.509  1.00  0.00              
ATOM    212  O   VAL   125      22.084  26.478  11.674  1.00  0.00              
ATOM    213  N   ARG   126      22.945  25.023  13.146  1.00  0.00              
ATOM    214  CA  ARG   126      24.351  25.359  12.999  1.00  0.00              
ATOM    215  C   ARG   126      24.945  24.848  11.711  1.00  0.00              
ATOM    216  O   ARG   126      25.998  25.351  11.286  1.00  0.00              
END
