REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0056AL009_4 
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  4   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1cuk 
ATOM      1  N   GLU    31     -22.292  -2.324 -14.055  1.00  0.00              
ATOM      2  CA  GLU    31     -21.946  -3.220 -15.170  1.00  0.00              
ATOM      3  C   GLU    31     -22.984  -3.166 -16.301  1.00  0.00              
ATOM      4  O   GLU    31     -22.664  -3.399 -17.472  1.00  0.00              
ATOM      5  N   ALA    32     -24.217  -2.856 -15.953  1.00  0.00              
ATOM      6  CA  ALA    32     -25.306  -2.809 -16.946  1.00  0.00              
ATOM      7  C   ALA    32     -25.069  -1.680 -17.960  1.00  0.00              
ATOM      8  O   ALA    32     -25.169  -1.883 -19.178  1.00  0.00              
ATOM      9  N   GLU    33     -24.759  -0.507 -17.439  1.00  0.00              
ATOM     10  CA  GLU    33     -24.497   0.676 -18.275  1.00  0.00              
ATOM     11  C   GLU    33     -23.266   0.433 -19.152  1.00  0.00              
ATOM     12  O   GLU    33     -23.221   0.848 -20.319  1.00  0.00              
ATOM     13  N   GLN    34     -22.268  -0.246 -18.636  1.00  0.00              
ATOM     14  CA  GLN    34     -21.061  -0.544 -19.398  1.00  0.00              
ATOM     15  C   GLN    34     -21.387  -1.459 -20.581  1.00  0.00              
ATOM     16  O   GLN    34     -20.900  -1.297 -21.712  1.00  0.00              
ATOM     17  N   SER    35     -22.228  -2.426 -20.297  1.00  0.00              
ATOM     18  CA  SER    35     -22.656  -3.372 -21.307  1.00  0.00              
ATOM     19  C   SER    35     -23.353  -2.657 -22.440  1.00  0.00              
ATOM     20  O   SER    35     -23.097  -2.882 -23.602  1.00  0.00              
ATOM     21  N   VAL    36     -24.250  -1.800 -22.073  1.00  0.00              
ATOM     22  CA  VAL    36     -25.004  -1.039 -23.041  1.00  0.00              
ATOM     23  C   VAL    36     -24.051  -0.244 -23.943  1.00  0.00              
ATOM     24  O   VAL    36     -24.225  -0.173 -25.167  1.00  0.00              
ATOM     25  N   LEU    37     -23.031   0.357 -23.293  1.00  0.00              
ATOM     26  CA  LEU    37     -22.002   1.147 -23.962  1.00  0.00              
ATOM     27  C   LEU    37     -21.232   0.246 -24.935  1.00  0.00              
ATOM     28  O   LEU    37     -21.076   0.560 -26.116  1.00  0.00              
ATOM     29  N   GLY    38     -20.771  -0.878 -24.410  1.00  0.00              
ATOM     30  CA  GLY    38     -20.045  -1.831 -25.196  1.00  0.00              
ATOM     31  C   GLY    38     -20.851  -2.235 -26.431  1.00  0.00              
ATOM     32  O   GLY    38     -20.342  -2.332 -27.535  1.00  0.00              
ATOM     33  N   GLY    39     -22.129  -2.450 -26.202  1.00  0.00              
ATOM     34  CA  GLY    39     -23.063  -2.835 -27.220  1.00  0.00              
ATOM     35  C   GLY    39     -23.180  -1.786 -28.291  1.00  0.00              
ATOM     36  O   GLY    39     -23.104  -2.078 -29.474  1.00  0.00              
ATOM     37  N   LEU    40     -23.372  -0.563 -27.864  1.00  0.00              
ATOM     38  CA  LEU    40     -23.494   0.564 -28.771  1.00  0.00              
ATOM     39  C   LEU    40     -22.274   0.726 -29.683  1.00  0.00              
ATOM     40  O   LEU    40     -22.374   0.908 -30.902  1.00  0.00              
ATOM     41  N   MET    41     -21.094   0.676 -29.079  1.00  0.00              
ATOM     42  CA  MET    41     -19.908   0.848 -29.858  1.00  0.00              
ATOM     43  C   MET    41     -19.601  -0.260 -30.872  1.00  0.00              
ATOM     44  O   MET    41     -18.914  -0.020 -31.804  1.00  0.00              
ATOM     45  N   LEU    42     -20.162  -1.478 -30.655  1.00  0.00              
ATOM     46  CA  LEU    42     -19.916  -2.599 -31.586  1.00  0.00              
ATOM     47  C   LEU    42     -20.564  -2.333 -32.949  1.00  0.00              
ATOM     48  O   LEU    42     -20.181  -2.950 -33.956  1.00  0.00              
ATOM     49  N   ASP    48     -21.466  -0.348 -36.439  1.00  0.00              
ATOM     50  CA  ASP    48     -20.688   0.329 -37.468  1.00  0.00              
ATOM     51  C   ASP    48     -20.744   1.820 -37.408  1.00  0.00              
ATOM     52  O   ASP    48     -19.774   2.515 -37.739  1.00  0.00              
ATOM     53  N   ASP    49     -21.876   2.306 -37.036  1.00  0.00              
ATOM     54  CA  ASP    49     -22.044   3.751 -37.011  1.00  0.00              
ATOM     55  C   ASP    49     -21.693   4.454 -35.690  1.00  0.00              
ATOM     56  O   ASP    49     -21.553   5.696 -35.678  1.00  0.00              
ATOM     57  N   VAL    50     -21.590   3.692 -34.588  1.00  0.00              
ATOM     58  CA  VAL    50     -21.311   4.345 -33.319  1.00  0.00              
ATOM     59  C   VAL    50     -19.934   4.042 -32.755  1.00  0.00              
ATOM     60  O   VAL    50     -19.517   2.901 -32.720  1.00  0.00              
ATOM     61  N   HIS    64     -16.995   5.410 -29.454  1.00  0.00              
ATOM     62  CA  HIS    64     -16.997   5.799 -28.031  1.00  0.00              
ATOM     63  C   HIS    64     -17.445   7.218 -27.748  1.00  0.00              
ATOM     64  O   HIS    64     -18.230   7.509 -26.817  1.00  0.00              
ATOM     65  N   ARG    65     -16.960   8.138 -28.537  1.00  0.00              
ATOM     66  CA  ARG    65     -17.368   9.495 -28.301  1.00  0.00              
ATOM     67  C   ARG    65     -18.860   9.714 -28.484  1.00  0.00              
ATOM     68  O   ARG    65     -19.508  10.432 -27.728  1.00  0.00              
ATOM     69  N   HIS    66     -19.442   9.104 -29.492  1.00  0.00              
ATOM     70  CA  HIS    66     -20.863   9.304 -29.670  1.00  0.00              
ATOM     71  C   HIS    66     -21.627   8.518 -28.630  1.00  0.00              
ATOM     72  O   HIS    66     -22.637   8.961 -28.115  1.00  0.00              
ATOM     73  N   ILE    67     -21.124   7.326 -28.312  1.00  0.00              
ATOM     74  CA  ILE    67     -21.797   6.536 -27.284  1.00  0.00              
ATOM     75  C   ILE    67     -21.848   7.342 -25.980  1.00  0.00              
ATOM     76  O   ILE    67     -22.845   7.365 -25.270  1.00  0.00              
ATOM     77  N   PHE    68     -20.767   8.053 -25.673  1.00  0.00              
ATOM     78  CA  PHE    68     -20.744   8.869 -24.473  1.00  0.00              
ATOM     79  C   PHE    68     -21.764  10.004 -24.557  1.00  0.00              
ATOM     80  O   PHE    68     -22.364  10.397 -23.564  1.00  0.00              
ATOM     81  N   THR    69     -21.962  10.543 -25.763  1.00  0.00              
ATOM     82  CA  THR    69     -22.932  11.622 -25.943  1.00  0.00              
ATOM     83  C   THR    69     -24.355  11.070 -25.814  1.00  0.00              
ATOM     84  O   THR    69     -25.214  11.672 -25.146  1.00  0.00              
ATOM     85  N   GLU    70     -24.608   9.889 -26.398  1.00  0.00              
ATOM     86  CA  GLU    70     -25.936   9.296 -26.262  1.00  0.00              
ATOM     87  C   GLU    70     -26.349   9.097 -24.773  1.00  0.00              
ATOM     88  O   GLU    70     -27.471   9.359 -24.360  1.00  0.00              
ATOM     89  N   MET    71     -25.419   8.625 -23.974  1.00  0.00              
ATOM     90  CA  MET    71     -25.653   8.378 -22.562  1.00  0.00              
ATOM     91  C   MET    71     -25.475   9.614 -21.668  1.00  0.00              
ATOM     92  O   MET    71     -25.574   9.535 -20.445  1.00  0.00              
ATOM     93  N   ALA    72     -25.269  10.764 -22.282  1.00  0.00              
ATOM     94  CA  ALA    72     -25.158  11.991 -21.550  1.00  0.00              
ATOM     95  C   ALA    72     -26.478  12.731 -21.727  1.00  0.00              
ATOM     96  O   ALA    72     -26.876  13.517 -20.891  1.00  0.00              
ATOM     97  N   ARG    73     -27.149  12.465 -22.854  1.00  0.00              
ATOM     98  CA  ARG    73     -28.441  13.090 -23.160  1.00  0.00              
ATOM     99  C   ARG    73     -29.572  12.304 -22.492  1.00  0.00              
ATOM    100  O   ARG    73     -30.585  12.847 -22.044  1.00  0.00              
ATOM    101  N   LEU    83     -29.326   5.109 -19.330  1.00  0.00              
ATOM    102  CA  LEU    83     -29.373   3.791 -19.949  1.00  0.00              
ATOM    103  C   LEU    83     -30.809   3.321 -20.124  1.00  0.00              
ATOM    104  O   LEU    83     -31.203   2.758 -21.168  1.00  0.00              
ATOM    105  N   ILE    84     -31.590   3.574 -19.064  1.00  0.00              
ATOM    106  CA  ILE    84     -33.011   3.229 -19.001  1.00  0.00              
ATOM    107  C   ILE    84     -33.812   3.885 -20.135  1.00  0.00              
ATOM    108  O   ILE    84     -34.443   3.200 -20.949  1.00  0.00              
ATOM    109  N   THR    85     -33.740   5.053 -20.190  1.00  0.00              
ATOM    110  CA  THR    85     -34.465   5.806 -21.219  1.00  0.00              
ATOM    111  C   THR    85     -34.024   5.362 -22.609  1.00  0.00              
ATOM    112  O   THR    85     -34.845   5.252 -23.530  1.00  0.00              
ATOM    113  N   LEU    86     -32.728   5.291 -22.741  1.00  0.00              
ATOM    114  CA  LEU    86     -32.225   4.852 -24.011  1.00  0.00              
ATOM    115  C   LEU    86     -32.837   3.551 -24.385  1.00  0.00              
ATOM    116  O   LEU    86     -33.313   3.377 -25.486  1.00  0.00              
ATOM    117  N   ALA    87     -32.818   2.625 -23.453  1.00  0.00              
ATOM    118  CA  ALA    87     -33.384   1.340 -23.708  1.00  0.00              
ATOM    119  C   ALA    87     -34.864   1.461 -24.091  1.00  0.00              
ATOM    120  O   ALA    87     -35.353   0.789 -24.987  1.00  0.00              
ATOM    121  N   GLU    88     -35.582   2.345 -23.432  1.00  0.00              
ATOM    122  CA  GLU    88     -36.996   2.529 -23.759  1.00  0.00              
ATOM    123  C   GLU    88     -37.167   3.017 -25.198  1.00  0.00              
ATOM    124  O   GLU    88     -37.909   2.432 -25.975  1.00  0.00              
ATOM    125  N   SER    89     -36.453   4.107 -25.529  1.00  0.00              
ATOM    126  CA  SER    89     -36.487   4.731 -26.860  1.00  0.00              
ATOM    127  C   SER    89     -36.355   3.720 -27.973  1.00  0.00              
ATOM    128  O   SER    89     -37.089   3.752 -28.936  1.00  0.00              
ATOM    129  N   LEU    90     -35.409   2.826 -27.810  1.00  0.00              
ATOM    130  CA  LEU    90     -35.149   1.769 -28.744  1.00  0.00              
ATOM    131  C   LEU    90     -36.321   0.800 -28.833  1.00  0.00              
ATOM    132  O   LEU    90     -36.760   0.435 -29.907  1.00  0.00              
ATOM    133  N   GLU    91     -36.795   0.358 -27.679  1.00  0.00              
ATOM    134  CA  GLU    91     -37.895  -0.583 -27.636  1.00  0.00              
ATOM    135  C   GLU    91     -39.146   0.018 -28.263  1.00  0.00              
ATOM    136  O   GLU    91     -39.861  -0.621 -29.050  1.00  0.00              
ATOM    137  N   TYR   104     -38.286   5.207 -31.037  1.00  0.00              
ATOM    138  CA  TYR   104     -38.504   6.657 -31.184  1.00  0.00              
ATOM    139  C   TYR   104     -37.217   7.340 -31.617  1.00  0.00              
ATOM    140  O   TYR   104     -36.526   7.961 -30.800  1.00  0.00              
ATOM    141  N   LEU   105     -37.162   7.326 -32.884  1.00  0.00              
ATOM    142  CA  LEU   105     -36.028   8.041 -33.505  1.00  0.00              
ATOM    143  C   LEU   105     -36.041   9.503 -33.163  1.00  0.00              
ATOM    144  O   LEU   105     -35.003  10.117 -32.876  1.00  0.00              
ATOM    145  N   ALA   106     -37.218  10.068 -33.202  1.00  0.00              
ATOM    146  CA  ALA   106     -37.338  11.456 -32.918  1.00  0.00              
ATOM    147  C   ALA   106     -36.277  11.880 -31.921  1.00  0.00              
ATOM    148  O   ALA   106     -35.392  12.694 -32.215  1.00  0.00              
ATOM    149  N   GLU   107     -36.382  11.308 -30.741  1.00  0.00              
ATOM    150  CA  GLU   107     -35.468  11.583 -29.643  1.00  0.00              
ATOM    151  C   GLU   107     -33.984  11.449 -30.009  1.00  0.00              
ATOM    152  O   GLU   107     -33.174  12.337 -29.746  1.00  0.00              
ATOM    153  N   LEU   108     -33.632  10.325 -30.610  1.00  0.00              
ATOM    154  CA  LEU   108     -32.253  10.084 -30.985  1.00  0.00              
ATOM    155  C   LEU   108     -31.647  11.154 -31.863  1.00  0.00              
ATOM    156  O   LEU   108     -30.513  11.541 -31.658  1.00  0.00              
ATOM    157  N   SER   109     -32.404  11.607 -32.860  1.00  0.00              
ATOM    158  CA  SER   109     -31.913  12.622 -33.794  1.00  0.00              
ATOM    159  C   SER   109     -31.491  13.922 -33.132  1.00  0.00              
ATOM    160  O   SER   109     -30.526  14.572 -33.581  1.00  0.00              
ATOM    161  N   LYS   110     -32.234  14.293 -32.069  1.00  0.00              
ATOM    162  CA  LYS   110     -31.978  15.492 -31.287  1.00  0.00              
ATOM    163  C   LYS   110     -30.525  15.516 -30.758  1.00  0.00              
ATOM    164  O   LYS   110     -30.150  16.381 -29.965  1.00  0.00              
ATOM    165  N   SER   119     -29.829  10.049 -38.971  1.00  0.00              
ATOM    166  CA  SER   119     -31.278   9.598 -39.085  1.00  0.00              
ATOM    167  C   SER   119     -31.320   8.135 -39.550  1.00  0.00              
ATOM    168  O   SER   119     -31.847   7.254 -38.858  1.00  0.00              
ATOM    169  N   ALA   120     -30.758   7.891 -40.723  1.00  0.00              
ATOM    170  CA  ALA   120     -30.654   6.523 -41.252  1.00  0.00              
ATOM    171  C   ALA   120     -29.873   5.675 -40.243  1.00  0.00              
ATOM    172  O   ALA   120     -30.175   4.498 -40.014  1.00  0.00              
ATOM    173  N   TYR   121     -29.045   6.547 -39.504  1.00  0.00              
ATOM    174  CA  TYR   121     -28.198   6.062 -38.416  1.00  0.00              
ATOM    175  C   TYR   121     -29.100   5.723 -37.219  1.00  0.00              
ATOM    176  O   TYR   121     -29.062   4.614 -36.671  1.00  0.00              
ATOM    177  N   ALA   122     -29.925   6.706 -36.869  1.00  0.00              
ATOM    178  CA  ALA   122     -30.872   6.566 -35.797  1.00  0.00              
ATOM    179  C   ALA   122     -31.737   5.348 -36.089  1.00  0.00              
ATOM    180  O   ALA   122     -31.852   4.416 -35.281  1.00  0.00              
ATOM    181  N   ASP   123     -32.315   5.348 -37.278  1.00  0.00              
ATOM    182  CA  ASP   123     -33.146   4.246 -37.663  1.00  0.00              
ATOM    183  C   ASP   123     -32.421   2.945 -37.566  1.00  0.00              
ATOM    184  O   ASP   123     -32.909   1.981 -36.954  1.00  0.00              
ATOM    185  N   ILE   124     -31.246   2.904 -38.170  1.00  0.00              
ATOM    186  CA  ILE   124     -30.461   1.673 -38.154  1.00  0.00              
ATOM    187  C   ILE   124     -30.132   1.216 -36.769  1.00  0.00              
ATOM    188  O   ILE   124     -30.114   0.019 -36.461  1.00  0.00              
ATOM    189  N   VAL   125     -29.858   2.194 -35.939  1.00  0.00              
ATOM    190  CA  VAL   125     -29.504   1.945 -34.564  1.00  0.00              
ATOM    191  C   VAL   125     -30.550   1.137 -33.853  1.00  0.00              
ATOM    192  O   VAL   125     -30.268   0.024 -33.332  1.00  0.00              
ATOM    193  N   ARG   126     -31.753   1.731 -33.852  1.00  0.00              
ATOM    194  CA  ARG   126     -32.953   1.183 -33.217  1.00  0.00              
ATOM    195  C   ARG   126     -33.135  -0.246 -33.586  1.00  0.00              
ATOM    196  O   ARG   126     -33.276  -1.170 -32.770  1.00  0.00              
ATOM    197  N   GLU   127     -33.103  -0.429 -34.859  1.00  0.00              
ATOM    198  CA  GLU   127     -33.266  -1.702 -35.426  1.00  0.00              
ATOM    199  C   GLU   127     -32.248  -2.625 -34.891  1.00  0.00              
ATOM    200  O   GLU   127     -32.558  -3.714 -34.447  1.00  0.00              
ATOM    201  N   ARG   128     -31.013  -2.182 -34.921  1.00  0.00              
ATOM    202  CA  ARG   128     -29.928  -2.992 -34.450  1.00  0.00              
ATOM    203  C   ARG   128     -29.905  -3.297 -32.987  1.00  0.00              
ATOM    204  O   ARG   128     -29.679  -4.439 -32.580  1.00  0.00              
ATOM    205  N   ALA   129     -30.088  -2.274 -32.210  1.00  0.00              
ATOM    206  CA  ALA   129     -30.083  -2.445 -30.794  1.00  0.00              
ATOM    207  C   ALA   129     -31.288  -3.253 -30.405  1.00  0.00              
ATOM    208  O   ALA   129     -31.217  -4.180 -29.595  1.00  0.00              
ATOM    209  N   VAL   130     -32.402  -2.875 -31.054  1.00  0.00              
ATOM    210  CA  VAL   130     -33.586  -3.588 -30.559  1.00  0.00              
ATOM    211  C   VAL   130     -33.357  -5.096 -30.617  1.00  0.00              
ATOM    212  O   VAL   130     -33.923  -5.862 -29.823  1.00  0.00              
ATOM    213  N   VAL   131     -32.521  -5.471 -31.558  1.00  0.00              
ATOM    214  CA  VAL   131     -32.196  -6.875 -31.818  1.00  0.00              
ATOM    215  C   VAL   131     -31.205  -7.433 -30.799  1.00  0.00              
ATOM    216  O   VAL   131     -31.365  -8.551 -30.293  1.00  0.00              
ATOM    217  N   ARG   132     -30.190  -6.652 -30.521  1.00  0.00              
ATOM    218  CA  ARG   132     -29.130  -7.066 -29.597  1.00  0.00              
ATOM    219  C   ARG   132     -29.682  -7.228 -28.182  1.00  0.00              
ATOM    220  O   ARG   132     -29.391  -8.225 -27.501  1.00  0.00              
END
