REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL009_5 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0065  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0065, chain B (SinI) of complex formed by SinR and SinI   
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: 1a0p 
ATOM      1  N   GLN B   6       8.332 -47.505  19.601  1.00  0.00              
ATOM      2  CA  GLN B   6       7.370 -47.851  20.649  1.00  0.00              
ATOM      3  C   GLN B   6       7.067 -49.339  20.634  1.00  0.00              
ATOM      4  O   GLN B   6       6.631 -49.892  21.627  1.00  0.00              
ATOM      5  N   GLU B   7       7.163 -49.940  19.462  1.00  0.00              
ATOM      6  CA  GLU B   7       7.257 -51.353  19.250  1.00  0.00              
ATOM      7  C   GLU B   7       8.334 -51.984  20.140  1.00  0.00              
ATOM      8  O   GLU B   7       8.088 -52.557  21.206  1.00  0.00              
ATOM      9  N   HIS B   8       9.586 -51.752  19.695  1.00  0.00              
ATOM     10  CA  HIS B   8      10.722 -52.365  20.375  1.00  0.00              
ATOM     11  C   HIS B   8      10.691 -51.998  21.847  1.00  0.00              
ATOM     12  O   HIS B   8      10.592 -52.932  22.654  1.00  0.00              
ATOM     13  N   PHE B   9      10.197 -50.813  22.191  1.00  0.00              
ATOM     14  CA  PHE B   9       9.938 -50.438  23.573  1.00  0.00              
ATOM     15  C   PHE B   9       8.924 -51.268  24.297  1.00  0.00              
ATOM     16  O   PHE B   9       9.136 -51.685  25.428  1.00  0.00              
ATOM     17  N   GLU B  10       7.847 -51.660  23.638  1.00  0.00              
ATOM     18  CA  GLU B  10       6.727 -52.353  24.291  1.00  0.00              
ATOM     19  C   GLU B  10       7.059 -53.846  24.284  1.00  0.00              
ATOM     20  O   GLU B  10       6.826 -54.502  25.307  1.00  0.00              
ATOM     21  N   LEU B  11       7.815 -54.212  23.237  1.00  0.00              
ATOM     22  CA  LEU B  11       8.425 -55.560  23.270  1.00  0.00              
ATOM     23  C   LEU B  11       9.369 -55.673  24.476  1.00  0.00              
ATOM     24  O   LEU B  11       9.062 -56.458  25.413  1.00  0.00              
ATOM     25  N   ASP B  12      10.149 -54.628  24.769  1.00  0.00              
ATOM     26  CA  ASP B  12      10.861 -54.578  26.034  1.00  0.00              
ATOM     27  C   ASP B  12       9.957 -54.487  27.235  1.00  0.00              
ATOM     28  O   ASP B  12      10.323 -55.150  28.234  1.00  0.00              
ATOM     29  N   GLN B  13       8.872 -53.693  27.226  1.00  0.00              
ATOM     30  CA  GLN B  13       8.114 -53.631  28.516  1.00  0.00              
ATOM     31  C   GLN B  13       7.672 -55.039  28.905  1.00  0.00              
ATOM     32  O   GLN B  13       7.498 -55.456  30.030  1.00  0.00              
ATOM     33  N   GLU B  14       7.076 -55.659  27.914  1.00  0.00              
ATOM     34  CA  GLU B  14       6.622 -57.025  27.862  1.00  0.00              
ATOM     35  C   GLU B  14       7.629 -58.022  28.426  1.00  0.00              
ATOM     36  O   GLU B  14       7.422 -58.680  29.471  1.00  0.00              
ATOM     37  N   TRP B  15       8.763 -58.115  27.727  1.00  0.00              
ATOM     38  CA  TRP B  15       9.810 -59.070  28.090  1.00  0.00              
ATOM     39  C   TRP B  15      10.344 -58.872  29.496  1.00  0.00              
ATOM     40  O   TRP B  15      10.473 -59.833  30.258  1.00  0.00              
ATOM     41  N   VAL B  16      10.542 -57.613  29.894  1.00  0.00              
ATOM     42  CA  VAL B  16      11.080 -57.314  31.223  1.00  0.00              
ATOM     43  C   VAL B  16      10.065 -57.567  32.326  1.00  0.00              
ATOM     44  O   VAL B  16      10.427 -58.017  33.427  1.00  0.00              
ATOM     45  N   GLU B  17       8.783 -57.303  32.049  1.00  0.00              
ATOM     46  CA  GLU B  17       7.697 -57.549  33.004  1.00  0.00              
ATOM     47  C   GLU B  17       7.410 -59.036  33.202  1.00  0.00              
ATOM     48  O   GLU B  17       7.314 -59.467  34.359  1.00  0.00              
ATOM     49  N   LEU B  18       7.503 -59.827  32.127  1.00  0.00              
ATOM     50  CA  LEU B  18       7.506 -61.294  32.375  1.00  0.00              
ATOM     51  C   LEU B  18       8.703 -61.649  33.261  1.00  0.00              
ATOM     52  O   LEU B  18       8.533 -62.094  34.397  1.00  0.00              
ATOM     53  N   MET B  19       9.904 -61.220  32.827  1.00  0.00              
ATOM     54  CA  MET B  19      11.108 -61.312  33.623  1.00  0.00              
ATOM     55  C   MET B  19      10.990 -60.852  35.060  1.00  0.00              
ATOM     56  O   MET B  19      11.273 -61.699  35.911  1.00  0.00              
ATOM     57  N   VAL B  20      10.363 -59.737  35.434  1.00  0.00              
ATOM     58  CA  VAL B  20      10.275 -59.480  36.873  1.00  0.00              
ATOM     59  C   VAL B  20       9.208 -60.331  37.545  1.00  0.00              
ATOM     60  O   VAL B  20       9.348 -60.691  38.723  1.00  0.00              
ATOM     61  N   GLU B  21       8.161 -60.702  36.804  1.00  0.00              
ATOM     62  CA  GLU B  21       7.169 -61.649  37.318  1.00  0.00              
ATOM     63  C   GLU B  21       7.922 -62.916  37.733  1.00  0.00              
ATOM     64  O   GLU B  21       7.966 -63.357  38.869  1.00  0.00              
ATOM     65  N   ALA B  22       8.608 -63.422  36.715  1.00  0.00              
ATOM     66  CA  ALA B  22       9.399 -64.633  36.758  1.00  0.00              
ATOM     67  C   ALA B  22      10.328 -64.637  37.959  1.00  0.00              
ATOM     68  O   ALA B  22      10.242 -65.503  38.815  1.00  0.00              
ATOM     69  N   LYS B  23      11.109 -63.556  38.062  1.00  0.00              
ATOM     70  CA  LYS B  23      12.066 -63.429  39.141  1.00  0.00              
ATOM     71  C   LYS B  23      11.387 -63.334  40.497  1.00  0.00              
ATOM     72  O   LYS B  23      11.863 -63.890  41.487  1.00  0.00              
ATOM     73  N   GLU B  24      10.342 -62.521  40.570  1.00  0.00              
ATOM     74  CA  GLU B  24       9.677 -62.305  41.859  1.00  0.00              
ATOM     75  C   GLU B  24       9.071 -63.607  42.377  1.00  0.00              
ATOM     76  O   GLU B  24       9.493 -64.125  43.431  1.00  0.00              
ATOM     77  N   ALA B  25       8.425 -64.350  41.473  1.00  0.00              
ATOM     78  CA  ALA B  25       8.022 -65.722  41.720  1.00  0.00              
ATOM     79  C   ALA B  25       9.181 -66.552  42.266  1.00  0.00              
ATOM     80  O   ALA B  25       8.910 -67.305  43.210  1.00  0.00              
ATOM     81  N   PRO B  29      23.311 -63.879  37.261  1.00  0.00              
ATOM     82  CA  PRO B  29      23.457 -64.330  35.874  1.00  0.00              
ATOM     83  C   PRO B  29      22.886 -65.720  35.601  1.00  0.00              
ATOM     84  O   PRO B  29      22.568 -66.084  34.454  1.00  0.00              
ATOM     85  N   GLU B  30      22.946 -66.598  36.603  1.00  0.00              
ATOM     86  CA  GLU B  30      22.421 -67.954  36.541  1.00  0.00              
ATOM     87  C   GLU B  30      20.898 -68.024  36.486  1.00  0.00              
ATOM     88  O   GLU B  30      20.286 -68.706  35.649  1.00  0.00              
ATOM     89  N   GLU B  31      20.348 -67.117  37.293  1.00  0.00              
ATOM     90  CA  GLU B  31      18.922 -66.813  37.303  1.00  0.00              
ATOM     91  C   GLU B  31      18.514 -66.304  35.930  1.00  0.00              
ATOM     92  O   GLU B  31      17.749 -66.970  35.229  1.00  0.00              
ATOM     93  N   ILE B  32      19.355 -65.420  35.355  1.00  0.00              
ATOM     94  CA  ILE B  32      19.047 -64.893  34.032  1.00  0.00              
ATOM     95  C   ILE B  32      19.293 -65.960  32.996  1.00  0.00              
ATOM     96  O   ILE B  32      18.530 -66.046  32.028  1.00  0.00              
ATOM     97  N   ARG B  33      20.302 -66.800  33.175  1.00  0.00              
ATOM     98  CA  ARG B  33      20.528 -67.901  32.228  1.00  0.00              
ATOM     99  C   ARG B  33      19.354 -68.896  32.222  1.00  0.00              
ATOM    100  O   ARG B  33      18.815 -69.248  31.179  1.00  0.00              
ATOM    101  N   LYS B  34      18.892 -69.309  33.398  1.00  0.00              
ATOM    102  CA  LYS B  34      17.634 -70.040  33.500  1.00  0.00              
ATOM    103  C   LYS B  34      16.502 -69.403  32.712  1.00  0.00              
ATOM    104  O   LYS B  34      16.041 -69.949  31.700  1.00  0.00              
ATOM    105  N   TYR B  35      15.964 -68.262  33.103  1.00  0.00              
ATOM    106  CA  TYR B  35      14.862 -67.567  32.461  1.00  0.00              
ATOM    107  C   TYR B  35      14.828 -67.707  30.950  1.00  0.00              
ATOM    108  O   TYR B  35      13.804 -67.970  30.330  1.00  0.00              
ATOM    109  N   LEU B  36      15.943 -67.370  30.318  1.00  0.00              
ATOM    110  CA  LEU B  36      16.178 -67.408  28.897  1.00  0.00              
ATOM    111  C   LEU B  36      15.969 -68.793  28.285  1.00  0.00              
ATOM    112  O   LEU B  36      15.541 -68.957  27.143  1.00  0.00              
ATOM    113  N   LEU B  37      16.440 -69.799  28.997  1.00  0.00              
ATOM    114  CA  LEU B  37      16.194 -71.204  28.758  1.00  0.00              
ATOM    115  C   LEU B  37      14.713 -71.549  28.914  1.00  0.00              
ATOM    116  O   LEU B  37      14.169 -72.160  27.991  1.00  0.00              
END
