REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0064AL009_2_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0064  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0064, chain A (SinR) 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  2   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1hbg 
ATOM      1  N   THR A  68      13.713  31.195  18.092  1.00  0.00              
ATOM      2  CA  THR A  68      14.921  31.332  17.265  1.00  0.00              
ATOM      3  C   THR A  68      15.975  30.280  17.664  1.00  0.00              
ATOM      4  O   THR A  68      16.641  29.841  16.715  1.00  0.00              
ATOM      5  N   GLU A  69      16.072  29.914  18.921  1.00  0.00              
ATOM      6  CA  GLU A  69      17.052  28.928  19.371  1.00  0.00              
ATOM      7  C   GLU A  69      16.760  27.574  18.691  1.00  0.00              
ATOM      8  O   GLU A  69      17.688  26.912  18.212  1.00  0.00              
ATOM      9  N   TYR A  70      15.497  27.213  18.692  1.00  0.00              
ATOM     10  CA  TYR A  70      15.073  25.948  18.074  1.00  0.00              
ATOM     11  C   TYR A  70      15.305  25.982  16.552  1.00  0.00              
ATOM     12  O   TYR A  70      15.793  24.964  16.027  1.00  0.00              
ATOM     13  N   ASP A  71      14.952  27.095  15.897  1.00  0.00              
ATOM     14  CA  ASP A  71      15.173  27.158  14.435  1.00  0.00              
ATOM     15  C   ASP A  71      16.614  26.985  14.101  1.00  0.00              
ATOM     16  O   ASP A  71      16.949  26.301  13.082  1.00  0.00              
ATOM     17  N   GLY A  72      17.502  27.566  14.913  1.00  0.00              
ATOM     18  CA  GLY A  72      18.930  27.456  14.674  1.00  0.00              
ATOM     19  C   GLY A  72      19.406  26.010  14.719  1.00  0.00              
ATOM     20  O   GLY A  72      20.231  25.620  13.867  1.00  0.00              
ATOM     21  N   GLN A  73      18.995  25.266  15.716  1.00  0.00              
ATOM     22  CA  GLN A  73      19.425  23.842  15.894  1.00  0.00              
ATOM     23  C   GLN A  73      18.905  22.971  14.758  1.00  0.00              
ATOM     24  O   GLN A  73      19.613  22.078  14.260  1.00  0.00              
ATOM     25  N   LEU A  74      17.633  23.207  14.360  1.00  0.00              
ATOM     26  CA  LEU A  74      17.032  22.430  13.274  1.00  0.00              
ATOM     27  C   LEU A  74      17.770  22.649  11.962  1.00  0.00              
ATOM     28  O   LEU A  74      18.082  21.632  11.254  1.00  0.00              
ATOM     29  N   ASP A  75      18.003  23.901  11.664  1.00  0.00              
ATOM     30  CA  ASP A  75      18.731  24.272  10.423  1.00  0.00              
ATOM     31  C   ASP A  75      20.137  23.660  10.430  1.00  0.00              
ATOM     32  O   ASP A  75      20.451  23.075   9.325  1.00  0.00              
ATOM     33  N   SER A  76      20.866  23.727  11.478  1.00  0.00              
ATOM     34  CA  SER A  76      22.219  23.190  11.577  1.00  0.00              
ATOM     35  C   SER A  76      22.264  21.677  11.470  1.00  0.00              
ATOM     36  O   SER A  76      23.031  21.180  10.646  1.00  0.00              
ATOM     37  N   GLU A  77      21.410  20.973  12.238  1.00  0.00              
ATOM     38  CA  GLU A  77      21.427  19.513  12.185  1.00  0.00              
ATOM     39  C   GLU A  77      20.867  18.977  10.887  1.00  0.00              
ATOM     40  O   GLU A  77      21.283  17.842  10.496  1.00  0.00              
ATOM     41  N   TRP A  78      19.948  19.725  10.233  1.00  0.00              
ATOM     42  CA  TRP A  78      19.361  19.256   8.927  1.00  0.00              
ATOM     43  C   TRP A  78      20.477  19.038   7.946  1.00  0.00              
ATOM     44  O   TRP A  78      20.440  18.091   7.121  1.00  0.00              
ATOM     45  N   GLU A  79      21.518  19.903   7.923  1.00  0.00              
ATOM     46  CA  GLU A  79      22.627  19.704   6.964  1.00  0.00              
ATOM     47  C   GLU A  79      23.230  18.347   7.176  1.00  0.00              
ATOM     48  O   GLU A  79      23.557  17.692   6.124  1.00  0.00              
ATOM     49  N   LYS A  80      23.416  17.842   8.394  1.00  0.00              
ATOM     50  CA  LYS A  80      24.008  16.530   8.604  1.00  0.00              
ATOM     51  C   LYS A  80      22.984  15.443   8.378  1.00  0.00              
ATOM     52  O   LYS A  80      23.387  14.267   8.003  1.00  0.00              
ATOM     53  N   LEU A  81      21.718  15.666   8.646  1.00  0.00              
ATOM     54  CA  LEU A  81      20.675  14.662   8.433  1.00  0.00              
ATOM     55  C   LEU A  81      20.506  14.437   6.924  1.00  0.00              
ATOM     56  O   LEU A  81      20.355  13.260   6.453  1.00  0.00              
ATOM     57  N   VAL A  82      20.587  15.524   6.121  1.00  0.00              
ATOM     58  CA  VAL A  82      20.445  15.371   4.666  1.00  0.00              
ATOM     59  C   VAL A  82      21.667  14.582   4.073  1.00  0.00              
ATOM     60  O   VAL A  82      21.500  13.761   3.166  1.00  0.00              
ATOM     61  N   SER A  88      17.572  10.512   2.047  1.00  0.00              
ATOM     62  CA  SER A  88      16.865   9.294   1.606  1.00  0.00              
ATOM     63  C   SER A  88      17.157   8.106   2.494  1.00  0.00              
ATOM     64  O   SER A  88      16.136   7.332   2.785  1.00  0.00              
ATOM     65  N   GLY A  89      18.324   7.885   3.012  1.00  0.00              
ATOM     66  CA  GLY A  89      18.656   6.710   3.899  1.00  0.00              
ATOM     67  C   GLY A  89      17.919   6.856   5.220  1.00  0.00              
ATOM     68  O   GLY A  89      17.453   5.843   5.788  1.00  0.00              
ATOM     69  N   VAL A  90      17.694   8.065   5.716  1.00  0.00              
ATOM     70  CA  VAL A  90      16.972   8.318   6.955  1.00  0.00              
ATOM     71  C   VAL A  90      15.500   7.973   6.752  1.00  0.00              
ATOM     72  O   VAL A  90      14.845   7.425   7.616  1.00  0.00              
ATOM     73  N   SER A  91      14.987   8.364   5.566  1.00  0.00              
ATOM     74  CA  SER A  91      13.592   8.068   5.193  1.00  0.00              
ATOM     75  C   SER A  91      13.341   6.557   5.048  1.00  0.00              
ATOM     76  O   SER A  91      12.319   6.054   5.564  1.00  0.00              
ATOM     77  N   LYS A  92      14.339   5.891   4.484  1.00  0.00              
ATOM     78  CA  LYS A  92      14.113   4.396   4.357  1.00  0.00              
ATOM     79  C   LYS A  92      14.106   3.765   5.744  1.00  0.00              
ATOM     80  O   LYS A  92      13.270   2.927   6.040  1.00  0.00              
ATOM     81  N   LYS A  93      15.046   4.150   6.591  1.00  0.00              
ATOM     82  CA  LYS A  93      15.156   3.579   7.945  1.00  0.00              
ATOM     83  C   LYS A  93      13.903   3.904   8.734  1.00  0.00              
ATOM     84  O   LYS A  93      13.265   3.010   9.364  1.00  0.00              
ATOM     85  N   GLN A  94      13.443   5.142   8.692  1.00  0.00              
ATOM     86  CA  GLN A  94      12.224   5.546   9.402  1.00  0.00              
ATOM     87  C   GLN A  94      11.021   4.724   9.029  1.00  0.00              
ATOM     88  O   GLN A  94      10.261   4.188   9.902  1.00  0.00              
ATOM     89  N   PHE A  95      10.717   4.557   7.742  1.00  0.00              
ATOM     90  CA  PHE A  95       9.503   3.781   7.319  1.00  0.00              
ATOM     91  C   PHE A  95       9.666   2.303   7.470  1.00  0.00              
ATOM     92  O   PHE A  95       8.601   1.723   7.839  1.00  0.00              
ATOM     93  N   ARG A  96      10.874   1.781   7.239  1.00  0.00              
ATOM     94  CA  ARG A  96      11.024   0.301   7.390  1.00  0.00              
ATOM     95  C   ARG A  96      10.748  -0.059   8.818  1.00  0.00              
ATOM     96  O   ARG A  96       9.982  -0.995   9.169  1.00  0.00              
ATOM     97  N   GLU A  97      11.477   0.684   9.716  1.00  0.00              
ATOM     98  CA  GLU A  97      11.264   0.412  11.157  1.00  0.00              
ATOM     99  C   GLU A  97       9.857   0.694  11.613  1.00  0.00              
ATOM    100  O   GLU A  97       9.325  -0.083  12.429  1.00  0.00              
ATOM    101  N   PHE A  98       9.171   1.718  11.137  1.00  0.00              
ATOM    102  CA  PHE A  98       7.789   1.996  11.549  1.00  0.00              
ATOM    103  C   PHE A  98       6.891   0.804  11.169  1.00  0.00              
ATOM    104  O   PHE A  98       6.088   0.433  12.050  1.00  0.00              
ATOM    105  N   LEU A  99       7.022   0.304   9.944  1.00  0.00              
ATOM    106  CA  LEU A  99       6.193  -0.833   9.559  1.00  0.00              
ATOM    107  C   LEU A  99       6.619  -2.091  10.313  1.00  0.00              
ATOM    108  O   LEU A  99       5.672  -2.884  10.604  1.00  0.00              
ATOM    109  N   ASP A 100       7.862  -2.262  10.606  1.00  0.00              
ATOM    110  CA  ASP A 100       8.282  -3.515  11.366  1.00  0.00              
ATOM    111  C   ASP A 100       7.677  -3.416  12.766  1.00  0.00              
ATOM    112  O   ASP A 100       7.278  -4.498  13.287  1.00  0.00              
ATOM    113  N   TYR A 101       7.579  -2.282  13.415  1.00  0.00              
ATOM    114  CA  TYR A 101       7.005  -2.149  14.738  1.00  0.00              
ATOM    115  C   TYR A 101       5.478  -2.131  14.771  1.00  0.00              
ATOM    116  O   TYR A 101       4.838  -2.488  15.793  1.00  0.00              
END
