REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL009_3 
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ft1_A 
ATOM      1  N   LYS B   5      92.777  56.023  57.894  1.00  0.00              
ATOM      2  CA  LYS B   5      91.358  55.823  58.177  1.00  0.00              
ATOM      3  C   LYS B   5      91.141  55.699  59.677  1.00  0.00              
ATOM      4  O   LYS B   5      90.352  56.435  60.267  1.00  0.00              
ATOM      5  N   GLN B   6      91.914  54.815  60.295  1.00  0.00              
ATOM      6  CA  GLN B   6      91.837  54.576  61.730  1.00  0.00              
ATOM      7  C   GLN B   6      92.042  55.858  62.557  1.00  0.00              
ATOM      8  O   GLN B   6      91.221  56.180  63.414  1.00  0.00              
ATOM      9  N   GLU B   7      93.111  56.598  62.285  1.00  0.00              
ATOM     10  CA  GLU B   7      93.379  57.845  63.003  1.00  0.00              
ATOM     11  C   GLU B   7      92.187  58.810  62.903  1.00  0.00              
ATOM     12  O   GLU B   7      91.836  59.502  63.870  1.00  0.00              
ATOM     13  N   HIS B   8      91.551  58.832  61.737  1.00  0.00              
ATOM     14  CA  HIS B   8      90.421  59.716  61.502  1.00  0.00              
ATOM     15  C   HIS B   8      89.160  59.229  62.199  1.00  0.00              
ATOM     16  O   HIS B   8      88.507  60.001  62.897  1.00  0.00              
ATOM     17  N   PHE B   9      88.841  57.949  62.046  1.00  0.00              
ATOM     18  CA  PHE B   9      87.659  57.398  62.680  1.00  0.00              
ATOM     19  C   PHE B   9      87.744  57.646  64.173  1.00  0.00              
ATOM     20  O   PHE B   9      86.777  58.090  64.786  1.00  0.00              
ATOM     21  N   GLU B  10      88.922  57.445  64.746  1.00  0.00              
ATOM     22  CA  GLU B  10      89.088  57.667  66.169  1.00  0.00              
ATOM     23  C   GLU B  10      88.926  59.125  66.544  1.00  0.00              
ATOM     24  O   GLU B  10      88.386  59.429  67.612  1.00  0.00              
ATOM     25  N   LEU B  11      89.381  60.036  65.692  1.00  0.00              
ATOM     26  CA  LEU B  11      89.226  61.456  65.999  1.00  0.00              
ATOM     27  C   LEU B  11      87.750  61.842  65.944  1.00  0.00              
ATOM     28  O   LEU B  11      87.304  62.753  66.639  1.00  0.00              
ATOM     29  N   ASP B  12      87.005  61.141  65.101  1.00  0.00              
ATOM     30  CA  ASP B  12      85.590  61.396  64.927  1.00  0.00              
ATOM     31  C   ASP B  12      84.851  60.848  66.132  1.00  0.00              
ATOM     32  O   ASP B  12      84.246  61.612  66.884  1.00  0.00              
ATOM     33  N   GLN B  13      84.937  59.533  66.333  1.00  0.00              
ATOM     34  CA  GLN B  13      84.280  58.864  67.453  1.00  0.00              
ATOM     35  C   GLN B  13      84.526  59.572  68.792  1.00  0.00              
ATOM     36  O   GLN B  13      83.632  59.666  69.629  1.00  0.00              
ATOM     37  N   GLU B  14      85.723  60.106  68.971  1.00  0.00              
ATOM     38  CA  GLU B  14      86.051  60.821  70.186  1.00  0.00              
ATOM     39  C   GLU B  14      85.194  62.076  70.286  1.00  0.00              
ATOM     40  O   GLU B  14      84.560  62.333  71.311  1.00  0.00              
ATOM     41  N   TRP B  15      85.211  62.888  69.242  1.00  0.00              
ATOM     42  CA  TRP B  15      84.430  64.103  69.263  1.00  0.00              
ATOM     43  C   TRP B  15      82.964  63.747  69.403  1.00  0.00              
ATOM     44  O   TRP B  15      82.204  64.474  70.011  1.00  0.00              
ATOM     45  N   VAL B  16      82.571  62.602  68.878  1.00  0.00              
ATOM     46  CA  VAL B  16      81.189  62.196  68.997  1.00  0.00              
ATOM     47  C   VAL B  16      80.836  61.974  70.473  1.00  0.00              
ATOM     48  O   VAL B  16      79.833  62.527  70.944  1.00  0.00              
ATOM     49  N   GLU B  17      81.657  61.206  71.212  1.00  0.00              
ATOM     50  CA  GLU B  17      81.385  60.956  72.636  1.00  0.00              
ATOM     51  C   GLU B  17      81.480  62.216  73.479  1.00  0.00              
ATOM     52  O   GLU B  17      80.706  62.417  74.408  1.00  0.00              
ATOM     53  N   LEU B  18      82.418  63.077  73.134  1.00  0.00              
ATOM     54  CA  LEU B  18      82.577  64.341  73.818  1.00  0.00              
ATOM     55  C   LEU B  18      81.268  65.143  73.662  1.00  0.00              
ATOM     56  O   LEU B  18      80.816  65.816  74.601  1.00  0.00              
ATOM     57  N   MET B  19      80.648  65.050  72.484  1.00  0.00              
ATOM     58  CA  MET B  19      79.398  65.751  72.200  1.00  0.00              
ATOM     59  C   MET B  19      78.214  65.084  72.881  1.00  0.00              
ATOM     60  O   MET B  19      77.386  65.767  73.477  1.00  0.00              
ATOM     61  N   VAL B  20      78.146  63.762  72.808  1.00  0.00              
ATOM     62  CA  VAL B  20      77.057  63.022  73.429  1.00  0.00              
ATOM     63  C   VAL B  20      77.052  63.183  74.953  1.00  0.00              
ATOM     64  O   VAL B  20      76.014  63.483  75.565  1.00  0.00              
ATOM     65  N   GLU B  21      78.232  63.041  75.550  1.00  0.00              
ATOM     66  CA  GLU B  21      78.382  63.104  76.994  1.00  0.00              
ATOM     67  C   GLU B  21      78.646  64.435  77.640  1.00  0.00              
ATOM     68  O   GLU B  21      78.418  64.578  78.834  1.00  0.00              
ATOM     69  N   GLU B  30      72.458  63.905  72.541  1.00  0.00              
ATOM     70  CA  GLU B  30      73.179  62.678  72.806  1.00  0.00              
ATOM     71  C   GLU B  30      72.709  61.543  71.918  1.00  0.00              
ATOM     72  O   GLU B  30      73.490  60.692  71.512  1.00  0.00              
ATOM     73  N   GLU B  31      71.430  61.544  71.590  1.00  0.00              
ATOM     74  CA  GLU B  31      70.872  60.478  70.778  1.00  0.00              
ATOM     75  C   GLU B  31      71.370  60.544  69.334  1.00  0.00              
ATOM     76  O   GLU B  31      71.660  59.522  68.714  1.00  0.00              
ATOM     77  N   ILE B  32      71.522  61.761  68.834  1.00  0.00              
ATOM     78  CA  ILE B  32      71.977  61.990  67.478  1.00  0.00              
ATOM     79  C   ILE B  32      73.464  61.626  67.348  1.00  0.00              
ATOM     80  O   ILE B  32      73.856  60.853  66.456  1.00  0.00              
ATOM     81  N   ARG B  33      74.265  62.129  68.284  1.00  0.00              
ATOM     82  CA  ARG B  33      75.692  61.887  68.300  1.00  0.00              
ATOM     83  C   ARG B  33      76.038  60.435  68.516  1.00  0.00              
ATOM     84  O   ARG B  33      77.063  59.979  68.048  1.00  0.00              
ATOM     85  N   LYS B  34      75.203  59.706  69.240  1.00  0.00              
ATOM     86  CA  LYS B  34      75.444  58.281  69.433  1.00  0.00              
ATOM     87  C   LYS B  34      75.131  57.603  68.109  1.00  0.00              
ATOM     88  O   LYS B  34      75.704  56.576  67.770  1.00  0.00              
ATOM     89  N   TYR B  35      74.173  58.161  67.384  1.00  0.00              
ATOM     90  CA  TYR B  35      73.798  57.625  66.086  1.00  0.00              
ATOM     91  C   TYR B  35      74.954  57.872  65.107  1.00  0.00              
ATOM     92  O   TYR B  35      75.403  56.955  64.433  1.00  0.00              
ATOM     93  N   LEU B  36      75.445  59.108  65.063  1.00  0.00              
ATOM     94  CA  LEU B  36      76.551  59.470  64.192  1.00  0.00              
ATOM     95  C   LEU B  36      77.719  58.520  64.442  1.00  0.00              
ATOM     96  O   LEU B  36      78.067  57.709  63.580  1.00  0.00              
ATOM     97  N   LEU B  37      78.279  58.575  65.645  1.00  0.00              
ATOM     98  CA  LEU B  37      79.402  57.718  65.971  1.00  0.00              
ATOM     99  C   LEU B  37      79.156  56.288  65.553  1.00  0.00              
ATOM    100  O   LEU B  37      80.020  55.641  64.964  1.00  0.00              
ATOM    101  N   LEU B  38      77.945  55.823  65.799  1.00  0.00              
ATOM    102  CA  LEU B  38      77.558  54.471  65.469  1.00  0.00              
ATOM    103  C   LEU B  38      77.610  54.232  63.953  1.00  0.00              
ATOM    104  O   LEU B  38      78.008  53.155  63.497  1.00  0.00              
ATOM    105  N   ASN B  39      77.212  55.236  63.178  1.00  0.00              
ATOM    106  CA  ASN B  39      77.225  55.144  61.718  1.00  0.00              
ATOM    107  C   ASN B  39      78.649  55.118  61.195  1.00  0.00              
ATOM    108  O   ASN B  39      78.978  54.305  60.336  1.00  0.00              
ATOM    109  N   LYS B  40      79.494  55.993  61.737  1.00  0.00              
ATOM    110  CA  LYS B  40      80.905  56.054  61.360  1.00  0.00              
ATOM    111  C   LYS B  40      81.562  54.680  61.548  1.00  0.00              
ATOM    112  O   LYS B  40      82.270  54.190  60.654  1.00  0.00              
ATOM    113  N   LYS B  41      81.302  54.054  62.697  1.00  0.00              
ATOM    114  CA  LYS B  41      81.833  52.727  62.992  1.00  0.00              
ATOM    115  C   LYS B  41      81.267  51.728  61.996  1.00  0.00              
ATOM    116  O   LYS B  41      82.004  50.999  61.335  1.00  0.00              
ATOM    117  N   SER B  42      79.945  51.709  61.891  1.00  0.00              
ATOM    118  CA  SER B  42      79.252  50.791  61.004  1.00  0.00              
ATOM    119  C   SER B  42      79.798  50.732  59.584  1.00  0.00              
ATOM    120  O   SER B  42      79.572  49.744  58.877  1.00  0.00              
ATOM    121  N   ALA B  43      80.483  51.778  59.139  1.00  0.00              
ATOM    122  CA  ALA B  43      80.986  51.736  57.784  1.00  0.00              
ATOM    123  C   ALA B  43      82.436  52.098  57.584  1.00  0.00              
ATOM    124  O   ALA B  43      82.878  52.224  56.453  1.00  0.00              
ATOM    125  N   HIS B  44      83.189  52.279  58.655  1.00  0.00              
ATOM    126  CA  HIS B  44      84.595  52.604  58.486  1.00  0.00              
ATOM    127  C   HIS B  44      85.481  51.829  59.429  1.00  0.00              
ATOM    128  O   HIS B  44      86.611  52.230  59.676  1.00  0.00              
END
