REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL009_4 
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  4   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ae9_A 
ATOM      1  N   ASP B  12      24.784  36.689  23.849  1.00  0.00              
ATOM      2  CA  ASP B  12      25.982  37.416  24.247  1.00  0.00              
ATOM      3  C   ASP B  12      25.874  37.957  25.669  1.00  0.00              
ATOM      4  O   ASP B  12      26.818  37.825  26.445  1.00  0.00              
ATOM      5  N   GLN B  13      24.719  38.522  26.027  1.00  0.00              
ATOM      6  CA  GLN B  13      24.523  39.075  27.368  1.00  0.00              
ATOM      7  C   GLN B  13      24.636  37.991  28.431  1.00  0.00              
ATOM      8  O   GLN B  13      25.311  38.181  29.444  1.00  0.00              
ATOM      9  N   GLU B  14      23.996  36.847  28.185  1.00  0.00              
ATOM     10  CA  GLU B  14      24.016  35.711  29.116  1.00  0.00              
ATOM     11  C   GLU B  14      25.440  35.199  29.311  1.00  0.00              
ATOM     12  O   GLU B  14      25.843  34.884  30.430  1.00  0.00              
ATOM     13  N   TRP B  15      26.174  35.071  28.205  1.00  0.00              
ATOM     14  CA  TRP B  15      27.559  34.606  28.231  1.00  0.00              
ATOM     15  C   TRP B  15      28.421  35.583  29.030  1.00  0.00              
ATOM     16  O   TRP B  15      29.188  35.167  29.900  1.00  0.00              
ATOM     17  N   VAL B  16      28.265  36.881  28.768  1.00  0.00              
ATOM     18  CA  VAL B  16      29.030  37.897  29.490  1.00  0.00              
ATOM     19  C   VAL B  16      28.700  37.848  30.976  1.00  0.00              
ATOM     20  O   VAL B  16      29.595  37.987  31.820  1.00  0.00              
ATOM     21  N   GLU B  17      27.425  37.631  31.303  1.00  0.00              
ATOM     22  CA  GLU B  17      27.016  37.538  32.708  1.00  0.00              
ATOM     23  C   GLU B  17      27.738  36.368  33.362  1.00  0.00              
ATOM     24  O   GLU B  17      28.265  36.491  34.475  1.00  0.00              
ATOM     25  N   LEU B  18      27.780  35.241  32.655  1.00  0.00              
ATOM     26  CA  LEU B  18      28.458  34.051  33.157  1.00  0.00              
ATOM     27  C   LEU B  18      29.961  34.303  33.321  1.00  0.00              
ATOM     28  O   LEU B  18      30.556  33.879  34.309  1.00  0.00              
ATOM     29  N   MET B  19      30.570  35.005  32.369  1.00  0.00              
ATOM     30  CA  MET B  19      31.999  35.309  32.447  1.00  0.00              
ATOM     31  C   MET B  19      32.264  36.142  33.699  1.00  0.00              
ATOM     32  O   MET B  19      33.225  35.895  34.435  1.00  0.00              
ATOM     33  N   VAL B  20      31.379  37.102  33.955  1.00  0.00              
ATOM     34  CA  VAL B  20      31.500  37.984  35.111  1.00  0.00              
ATOM     35  C   VAL B  20      31.334  37.229  36.427  1.00  0.00              
ATOM     36  O   VAL B  20      32.168  37.329  37.327  1.00  0.00              
ATOM     37  N   GLU B  21      30.272  36.438  36.513  1.00  0.00              
ATOM     38  CA  GLU B  21      29.958  35.677  37.721  1.00  0.00              
ATOM     39  C   GLU B  21      30.895  34.501  38.014  1.00  0.00              
ATOM     40  O   GLU B  21      31.286  34.284  39.164  1.00  0.00              
ATOM     41  N   ALA B  22      31.277  33.771  36.969  1.00  0.00              
ATOM     42  CA  ALA B  22      32.124  32.584  37.103  1.00  0.00              
ATOM     43  C   ALA B  22      33.632  32.800  37.024  1.00  0.00              
ATOM     44  O   ALA B  22      34.389  32.137  37.729  1.00  0.00              
ATOM     45  N   PRO B  29      46.242  33.161  23.680  1.00  0.00              
ATOM     46  CA  PRO B  29      45.639  32.434  22.565  1.00  0.00              
ATOM     47  C   PRO B  29      46.073  30.967  22.545  1.00  0.00              
ATOM     48  O   PRO B  29      45.270  30.070  22.265  1.00  0.00              
ATOM     49  N   GLU B  30      47.349  30.732  22.838  1.00  0.00              
ATOM     50  CA  GLU B  30      47.877  29.380  22.846  1.00  0.00              
ATOM     51  C   GLU B  30      47.187  28.477  23.844  1.00  0.00              
ATOM     52  O   GLU B  30      46.878  27.326  23.542  1.00  0.00              
ATOM     53  N   GLU B  31      46.948  28.998  25.039  1.00  0.00              
ATOM     54  CA  GLU B  31      46.290  28.231  26.081  1.00  0.00              
ATOM     55  C   GLU B  31      44.848  27.891  25.691  1.00  0.00              
ATOM     56  O   GLU B  31      44.407  26.752  25.847  1.00  0.00              
ATOM     57  N   ILE B  32      44.127  28.871  25.165  1.00  0.00              
ATOM     58  CA  ILE B  32      42.743  28.655  24.759  1.00  0.00              
ATOM     59  C   ILE B  32      42.674  27.597  23.666  1.00  0.00              
ATOM     60  O   ILE B  32      41.888  26.659  23.759  1.00  0.00              
ATOM     61  N   ARG B  33      43.518  27.735  22.646  1.00  0.00              
ATOM     62  CA  ARG B  33      43.562  26.782  21.539  1.00  0.00              
ATOM     63  C   ARG B  33      43.899  25.371  22.011  1.00  0.00              
ATOM     64  O   ARG B  33      43.285  24.394  21.568  1.00  0.00              
ATOM     65  N   LYS B  34      44.865  25.284  22.924  1.00  0.00              
ATOM     66  CA  LYS B  34      45.334  24.019  23.481  1.00  0.00              
ATOM     67  C   LYS B  34      44.217  23.274  24.206  1.00  0.00              
ATOM     68  O   LYS B  34      44.017  22.075  23.994  1.00  0.00              
ATOM     69  N   TYR B  35      43.486  23.973  25.063  1.00  0.00              
ATOM     70  CA  TYR B  35      42.397  23.328  25.783  1.00  0.00              
ATOM     71  C   TYR B  35      41.234  22.942  24.859  1.00  0.00              
ATOM     72  O   TYR B  35      40.584  21.902  25.056  1.00  0.00              
ATOM     73  N   LEU B  36      40.987  23.771  23.847  1.00  0.00              
ATOM     74  CA  LEU B  36      39.941  23.492  22.871  1.00  0.00              
ATOM     75  C   LEU B  36      40.331  22.211  22.125  1.00  0.00              
ATOM     76  O   LEU B  36      39.506  21.314  21.940  1.00  0.00              
ATOM     77  N   LEU B  37      41.597  22.119  21.729  1.00  0.00              
ATOM     78  CA  LEU B  37      42.102  20.948  21.027  1.00  0.00              
ATOM     79  C   LEU B  37      41.886  19.674  21.856  1.00  0.00              
ATOM     80  O   LEU B  37      41.510  18.623  21.312  1.00  0.00              
ATOM     81  N   LEU B  38      42.089  19.771  23.172  1.00  0.00              
ATOM     82  CA  LEU B  38      41.899  18.620  24.050  1.00  0.00              
ATOM     83  C   LEU B  38      40.430  18.211  24.138  1.00  0.00              
ATOM     84  O   LEU B  38      40.117  17.017  24.123  1.00  0.00              
ATOM     85  N   ASN B  39      39.530  19.188  24.237  1.00  0.00              
ATOM     86  CA  ASN B  39      38.096  18.899  24.292  1.00  0.00              
ATOM     87  C   ASN B  39      37.678  18.269  22.953  1.00  0.00              
ATOM     88  O   ASN B  39      36.866  17.347  22.912  1.00  0.00              
ATOM     89  N   LYS B  40      38.252  18.762  21.861  1.00  0.00              
ATOM     90  CA  LYS B  40      37.954  18.240  20.532  1.00  0.00              
ATOM     91  C   LYS B  40      38.285  16.753  20.472  1.00  0.00              
ATOM     92  O   LYS B  40      37.486  15.953  19.976  1.00  0.00              
ATOM     93  N   LYS B  41      39.467  16.381  20.960  1.00  0.00              
ATOM     94  CA  LYS B  41      39.866  14.976  20.970  1.00  0.00              
ATOM     95  C   LYS B  41      38.917  14.161  21.843  1.00  0.00              
ATOM     96  O   LYS B  41      38.490  13.076  21.458  1.00  0.00              
ATOM     97  N   SER B  42      38.567  14.703  23.006  1.00  0.00              
ATOM     98  CA  SER B  42      37.669  14.028  23.937  1.00  0.00              
ATOM     99  C   SER B  42      36.302  13.704  23.340  1.00  0.00              
ATOM    100  O   SER B  42      35.690  12.712  23.728  1.00  0.00              
ATOM    101  N   ALA B  43      35.818  14.546  22.425  1.00  0.00              
ATOM    102  CA  ALA B  43      34.517  14.333  21.777  1.00  0.00              
ATOM    103  C   ALA B  43      34.519  13.091  20.883  1.00  0.00              
ATOM    104  O   ALA B  43      33.476  12.481  20.655  1.00  0.00              
END
