REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0064AL009_3 
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1rro 
ATOM      1  N   GLY A   3      30.570   2.966  30.825  1.00  0.00              
ATOM      2  CA  GLY A   3      31.094   3.968  29.922  1.00  0.00              
ATOM      3  C   GLY A   3      31.413   3.411  28.531  1.00  0.00              
ATOM      4  O   GLY A   3      31.232   4.113  27.535  1.00  0.00              
ATOM      5  N   GLN A   4      31.882   2.154  28.501  1.00  0.00              
ATOM      6  CA  GLN A   4      32.243   1.553  27.225  1.00  0.00              
ATOM      7  C   GLN A   4      31.026   1.316  26.317  1.00  0.00              
ATOM      8  O   GLN A   4      31.116   1.442  25.110  1.00  0.00              
ATOM      9  N   ARG A   5      29.929   0.943  26.989  1.00  0.00              
ATOM     10  CA  ARG A   5      28.688   0.675  26.193  1.00  0.00              
ATOM     11  C   ARG A   5      28.100   2.025  25.651  1.00  0.00              
ATOM     12  O   ARG A   5      27.625   2.051  24.541  1.00  0.00              
ATOM     13  N   ILE A   6      28.203   3.042  26.490  1.00  0.00              
ATOM     14  CA  ILE A   6      27.778   4.392  26.074  1.00  0.00              
ATOM     15  C   ILE A   6      28.623   4.851  24.868  1.00  0.00              
ATOM     16  O   ILE A   6      28.124   5.313  23.851  1.00  0.00              
ATOM     17  N   LYS A   7      29.965   4.687  24.983  1.00  0.00              
ATOM     18  CA  LYS A   7      30.888   5.028  23.900  1.00  0.00              
ATOM     19  C   LYS A   7      30.560   4.272  22.605  1.00  0.00              
ATOM     20  O   LYS A   7      30.527   4.832  21.500  1.00  0.00              
ATOM     21  N   GLN A   8      30.229   2.990  22.760  1.00  0.00              
ATOM     22  CA  GLN A   8      29.874   2.138  21.589  1.00  0.00              
ATOM     23  C   GLN A   8      28.565   2.654  20.939  1.00  0.00              
ATOM     24  O   GLN A   8      28.509   2.677  19.712  1.00  0.00              
ATOM     25  N   TYR A   9      27.653   3.000  21.810  1.00  0.00              
ATOM     26  CA  TYR A   9      26.310   3.478  21.280  1.00  0.00              
ATOM     27  C   TYR A   9      26.446   4.751  20.495  1.00  0.00              
ATOM     28  O   TYR A   9      25.819   4.945  19.421  1.00  0.00              
ATOM     29  N   ARG A  10      27.301   5.671  20.976  1.00  0.00              
ATOM     30  CA  ARG A  10      27.527   6.957  20.296  1.00  0.00              
ATOM     31  C   ARG A  10      28.283   6.769  18.991  1.00  0.00              
ATOM     32  O   ARG A  10      28.044   7.403  17.988  1.00  0.00              
ATOM     33  N   LYS A  11      29.258   5.830  19.067  1.00  0.00              
ATOM     34  CA  LYS A  11      30.051   5.497  17.857  1.00  0.00              
ATOM     35  C   LYS A  11      29.171   5.019  16.707  1.00  0.00              
ATOM     36  O   LYS A  11      29.305   5.348  15.538  1.00  0.00              
ATOM     37  N   GLU A  12      28.202   4.139  17.085  1.00  0.00              
ATOM     38  CA  GLU A  12      27.264   3.536  16.143  1.00  0.00              
ATOM     39  C   GLU A  12      26.435   4.568  15.380  1.00  0.00              
ATOM     40  O   GLU A  12      26.089   4.343  14.226  1.00  0.00              
ATOM     41  N   LEU A  17      16.357   4.518  17.628  1.00  0.00              
ATOM     42  CA  LEU A  17      16.116   4.283  19.045  1.00  0.00              
ATOM     43  C   LEU A  17      16.466   2.874  19.499  1.00  0.00              
ATOM     44  O   LEU A  17      17.198   2.676  20.491  1.00  0.00              
ATOM     45  N   SER A  18      15.919   1.881  18.814  1.00  0.00              
ATOM     46  CA  SER A  18      16.122   0.478  19.244  1.00  0.00              
ATOM     47  C   SER A  18      17.592   0.093  19.276  1.00  0.00              
ATOM     48  O   SER A  18      17.974  -0.679  20.160  1.00  0.00              
ATOM     49  N   GLU A  19      18.325   0.560  18.271  1.00  0.00              
ATOM     50  CA  GLU A  19      19.793   0.190  18.278  1.00  0.00              
ATOM     51  C   GLU A  19      20.503   0.857  19.443  1.00  0.00              
ATOM     52  O   GLU A  19      21.339   0.220  20.061  1.00  0.00              
ATOM     53  N   LEU A  20      20.176   2.109  19.665  1.00  0.00              
ATOM     54  CA  LEU A  20      20.845   2.841  20.771  1.00  0.00              
ATOM     55  C   LEU A  20      20.580   2.160  22.093  1.00  0.00              
ATOM     56  O   LEU A  20      21.463   1.976  22.950  1.00  0.00              
ATOM     57  N   ALA A  21      19.273   1.821  22.282  1.00  0.00              
ATOM     58  CA  ALA A  21      18.896   1.179  23.584  1.00  0.00              
ATOM     59  C   ALA A  21      19.560  -0.200  23.757  1.00  0.00              
ATOM     60  O   ALA A  21      19.887  -0.519  24.917  1.00  0.00              
ATOM     61  N   GLU A  22      19.733  -0.918  22.660  1.00  0.00              
ATOM     62  CA  GLU A  22      20.438  -2.232  22.774  1.00  0.00              
ATOM     63  C   GLU A  22      21.953  -2.086  23.035  1.00  0.00              
ATOM     64  O   GLU A  22      22.505  -2.653  24.008  1.00  0.00              
ATOM     65  N   LYS A  23      22.593  -1.283  22.181  1.00  0.00              
ATOM     66  CA  LYS A  23      24.064  -1.130  22.329  1.00  0.00              
ATOM     67  C   LYS A  23      24.506  -0.529  23.619  1.00  0.00              
ATOM     68  O   LYS A  23      25.507  -0.964  24.236  1.00  0.00              
ATOM     69  N   ALA A  24      23.718   0.462  24.109  1.00  0.00              
ATOM     70  CA  ALA A  24      24.040   1.153  25.363  1.00  0.00              
ATOM     71  C   ALA A  24      23.808   0.266  26.609  1.00  0.00              
ATOM     72  O   ALA A  24      24.322   0.622  27.655  1.00  0.00              
ATOM     73  N   LYS A  28      13.204  -1.734  35.601  1.00  0.00              
ATOM     74  CA  LYS A  28      12.325  -0.526  35.529  1.00  0.00              
ATOM     75  C   LYS A  28      12.908   0.588  36.425  1.00  0.00              
ATOM     76  O   LYS A  28      12.895   1.786  35.973  1.00  0.00              
ATOM     77  N   SER A  29      13.370   0.312  37.595  1.00  0.00              
ATOM     78  CA  SER A  29      13.896   1.314  38.501  1.00  0.00              
ATOM     79  C   SER A  29      15.099   2.053  37.883  1.00  0.00              
ATOM     80  O   SER A  29      15.229   3.315  37.964  1.00  0.00              
ATOM     81  N   TYR A  30      15.972   1.280  37.266  1.00  0.00              
ATOM     82  CA  TYR A  30      17.168   1.860  36.590  1.00  0.00              
ATOM     83  C   TYR A  30      16.757   2.663  35.396  1.00  0.00              
ATOM     84  O   TYR A  30      17.364   3.781  35.205  1.00  0.00              
ATOM     85  N   LEU A  31      15.835   2.245  34.603  1.00  0.00              
ATOM     86  CA  LEU A  31      15.356   2.991  33.441  1.00  0.00              
ATOM     87  C   LEU A  31      14.700   4.303  33.926  1.00  0.00              
ATOM     88  O   LEU A  31      14.999   5.358  33.258  1.00  0.00              
ATOM     89  N   SER A  32      13.999   4.306  34.996  1.00  0.00              
ATOM     90  CA  SER A  32      13.394   5.512  35.567  1.00  0.00              
ATOM     91  C   SER A  32      14.494   6.480  36.036  1.00  0.00              
ATOM     92  O   SER A  32      14.302   7.737  35.754  1.00  0.00              
ATOM     93  N   SER A  33      15.554   6.006  36.624  1.00  0.00              
ATOM     94  CA  SER A  33      16.653   6.919  37.025  1.00  0.00              
ATOM     95  C   SER A  33      17.233   7.562  35.772  1.00  0.00              
ATOM     96  O   SER A  33      17.505   8.807  35.794  1.00  0.00              
ATOM     97  N   ILE A  34      17.426   6.853  34.689  1.00  0.00              
ATOM     98  CA  ILE A  34      17.926   7.426  33.454  1.00  0.00              
ATOM     99  C   ILE A  34      16.920   8.440  32.945  1.00  0.00              
ATOM    100  O   ILE A  34      17.346   9.566  32.514  1.00  0.00              
ATOM    101  N   GLU A  35      15.662   8.132  32.887  1.00  0.00              
ATOM    102  CA  GLU A  35      14.604   9.071  32.460  1.00  0.00              
ATOM    103  C   GLU A  35      14.738  10.424  33.235  1.00  0.00              
ATOM    104  O   GLU A  35      14.704  11.484  32.565  1.00  0.00              
ATOM    105  N   ARG A  36      14.902  10.329  34.485  1.00  0.00              
ATOM    106  CA  ARG A  36      15.017  11.572  35.325  1.00  0.00              
ATOM    107  C   ARG A  36      16.209  12.367  34.894  1.00  0.00              
ATOM    108  O   ARG A  36      16.048  13.631  34.840  1.00  0.00              
ATOM    109  N   ASN A  37      17.297  11.797  34.504  1.00  0.00              
ATOM    110  CA  ASN A  37      18.484  12.592  34.055  1.00  0.00              
ATOM    111  C   ASN A  37      18.240  13.203  32.742  1.00  0.00              
ATOM    112  O   ASN A  37      18.782  14.320  32.421  1.00  0.00              
ATOM    113  N   LEU A  38      17.444  12.642  31.845  1.00  0.00              
ATOM    114  CA  LEU A  38      17.160  13.154  30.521  1.00  0.00              
ATOM    115  C   LEU A  38      16.145  14.297  30.543  1.00  0.00              
ATOM    116  O   LEU A  38      16.147  15.201  29.703  1.00  0.00              
ATOM    117  N   GLU A  48      13.331  20.546  23.216  1.00  0.00              
ATOM    118  CA  GLU A  48      14.790  20.514  23.156  1.00  0.00              
ATOM    119  C   GLU A  48      15.362  19.282  23.810  1.00  0.00              
ATOM    120  O   GLU A  48      16.527  18.927  23.515  1.00  0.00              
ATOM    121  N   LYS A  49      14.674  18.623  24.752  1.00  0.00              
ATOM    122  CA  LYS A  49      15.211  17.468  25.431  1.00  0.00              
ATOM    123  C   LYS A  49      15.474  16.354  24.440  1.00  0.00              
ATOM    124  O   LYS A  49      16.419  15.518  24.695  1.00  0.00              
ATOM    125  N   VAL A  50      14.737  16.255  23.369  1.00  0.00              
ATOM    126  CA  VAL A  50      14.961  15.250  22.334  1.00  0.00              
ATOM    127  C   VAL A  50      16.199  15.606  21.509  1.00  0.00              
ATOM    128  O   VAL A  50      17.017  14.727  21.196  1.00  0.00              
ATOM    129  N   SER A  51      16.305  16.858  21.121  1.00  0.00              
ATOM    130  CA  SER A  51      17.463  17.311  20.308  1.00  0.00              
ATOM    131  C   SER A  51      18.767  17.090  21.080  1.00  0.00              
ATOM    132  O   SER A  51      19.751  16.701  20.391  1.00  0.00              
ATOM    133  N   SER A  76      16.316  16.814  13.090  1.00  0.00              
ATOM    134  CA  SER A  76      14.810  16.916  13.225  1.00  0.00              
ATOM    135  C   SER A  76      14.242  15.545  12.873  1.00  0.00              
ATOM    136  O   SER A  76      13.235  15.156  13.578  1.00  0.00              
ATOM    137  N   GLU A  77      14.759  14.882  11.898  1.00  0.00              
ATOM    138  CA  GLU A  77      14.218  13.565  11.506  1.00  0.00              
ATOM    139  C   GLU A  77      14.420  12.563  12.654  1.00  0.00              
ATOM    140  O   GLU A  77      13.512  11.713  12.925  1.00  0.00              
ATOM    141  N   TRP A  78      15.600  12.565  13.287  1.00  0.00              
ATOM    142  CA  TRP A  78      15.855  11.680  14.395  1.00  0.00              
ATOM    143  C   TRP A  78      15.000  11.935  15.640  1.00  0.00              
ATOM    144  O   TRP A  78      14.561  10.998  16.321  1.00  0.00              
ATOM    145  N   GLU A  79      14.708  13.227  15.847  1.00  0.00              
ATOM    146  CA  GLU A  79      13.824  13.532  17.025  1.00  0.00              
ATOM    147  C   GLU A  79      12.395  13.004  16.712  1.00  0.00              
ATOM    148  O   GLU A  79      11.745  12.451  17.642  1.00  0.00              
ATOM    149  N   LYS A  80      11.995  13.189  15.511  1.00  0.00              
ATOM    150  CA  LYS A  80      10.647  12.646  15.107  1.00  0.00              
ATOM    151  C   LYS A  80      10.669  11.168  15.275  1.00  0.00              
ATOM    152  O   LYS A  80       9.622  10.630  15.786  1.00  0.00              
ATOM    153  N   LEU A  81      11.702  10.435  14.923  1.00  0.00              
ATOM    154  CA  LEU A  81      11.761   8.968  15.071  1.00  0.00              
ATOM    155  C   LEU A  81      11.633   8.599  16.524  1.00  0.00              
ATOM    156  O   LEU A  81      10.930   7.564  16.846  1.00  0.00              
ATOM    157  N   VAL A  82      12.211   9.292  17.440  1.00  0.00              
ATOM    158  CA  VAL A  82      12.114   9.050  18.843  1.00  0.00              
ATOM    159  C   VAL A  82      10.644   9.186  19.327  1.00  0.00              
ATOM    160  O   VAL A  82      10.122   8.341  20.080  1.00  0.00              
ATOM    161  N   ARG A  83      10.035  10.303  18.921  1.00  0.00              
ATOM    162  CA  ARG A  83       8.607  10.540  19.279  1.00  0.00              
ATOM    163  C   ARG A  83       7.731   9.474  18.664  1.00  0.00              
ATOM    164  O   ARG A  83       6.797   8.968  19.360  1.00  0.00              
ATOM    165  N   ASP A  84       7.937   9.124  17.441  1.00  0.00              
ATOM    166  CA  ASP A  84       7.117   8.067  16.769  1.00  0.00              
ATOM    167  C   ASP A  84       7.293   6.729  17.527  1.00  0.00              
ATOM    168  O   ASP A  84       6.311   5.911  17.631  1.00  0.00              
ATOM    169  N   ALA A  85       8.501   6.465  18.015  1.00  0.00              
ATOM    170  CA  ALA A  85       8.751   5.188  18.681  1.00  0.00              
ATOM    171  C   ALA A  85       8.077   5.134  20.034  1.00  0.00              
ATOM    172  O   ALA A  85       7.659   4.026  20.463  1.00  0.00              
ATOM    173  N   MET A  86       7.926   6.283  20.727  1.00  0.00              
ATOM    174  CA  MET A  86       7.440   6.263  22.068  1.00  0.00              
ATOM    175  C   MET A  86       5.999   6.689  22.372  1.00  0.00              
ATOM    176  O   MET A  86       5.447   6.125  23.282  1.00  0.00              
ATOM    177  N   LYS A  92       7.148   8.896  31.535  1.00  0.00              
ATOM    178  CA  LYS A  92       8.061   7.846  32.056  1.00  0.00              
ATOM    179  C   LYS A  92       7.573   6.491  31.632  1.00  0.00              
ATOM    180  O   LYS A  92       8.413   5.578  31.313  1.00  0.00              
ATOM    181  N   LYS A  93       6.284   6.240  31.620  1.00  0.00              
ATOM    182  CA  LYS A  93       5.680   4.926  31.266  1.00  0.00              
ATOM    183  C   LYS A  93       5.998   4.606  29.829  1.00  0.00              
ATOM    184  O   LYS A  93       6.412   3.478  29.453  1.00  0.00              
ATOM    185  N   GLN A  94       5.836   5.578  28.936  1.00  0.00              
ATOM    186  CA  GLN A  94       6.110   5.433  27.532  1.00  0.00              
ATOM    187  C   GLN A  94       7.603   5.133  27.290  1.00  0.00              
ATOM    188  O   GLN A  94       7.962   4.370  26.375  1.00  0.00              
ATOM    189  N   PHE A  95       8.436   5.805  28.064  1.00  0.00              
ATOM    190  CA  PHE A  95       9.884   5.590  27.980  1.00  0.00              
ATOM    191  C   PHE A  95      10.211   4.103  28.323  1.00  0.00              
ATOM    192  O   PHE A  95      10.966   3.483  27.571  1.00  0.00              
ATOM    193  N   ARG A  96       9.648   3.647  29.424  1.00  0.00              
ATOM    194  CA  ARG A  96       9.879   2.242  29.840  1.00  0.00              
ATOM    195  C   ARG A  96       9.439   1.294  28.717  1.00  0.00              
ATOM    196  O   ARG A  96      10.198   0.340  28.391  1.00  0.00              
ATOM    197  N   GLU A  97       8.273   1.510  28.191  1.00  0.00              
ATOM    198  CA  GLU A  97       7.749   0.611  27.124  1.00  0.00              
ATOM    199  C   GLU A  97       8.628   0.657  25.932  1.00  0.00              
ATOM    200  O   GLU A  97       8.951  -0.420  25.292  1.00  0.00              
ATOM    201  N   PHE A  98       9.169   1.786  25.509  1.00  0.00              
ATOM    202  CA  PHE A  98       9.995   1.923  24.341  1.00  0.00              
ATOM    203  C   PHE A  98      11.361   1.189  24.550  1.00  0.00              
ATOM    204  O   PHE A  98      11.769   0.443  23.680  1.00  0.00              
ATOM    205  N   LEU A  99      11.944   1.431  25.688  1.00  0.00              
ATOM    206  CA  LEU A  99      13.277   0.874  25.980  1.00  0.00              
ATOM    207  C   LEU A  99      13.224  -0.638  25.929  1.00  0.00              
ATOM    208  O   LEU A  99      14.245  -1.190  25.501  1.00  0.00              
END
