REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL009_2 
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  2   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2wrp_R 
ATOM      1  N   ASN B   3      -6.761  11.027   5.669  1.00  0.00              
ATOM      2  CA  ASN B   3      -8.022  10.880   4.948  1.00  0.00              
ATOM      3  C   ASN B   3      -7.878  11.443   3.523  1.00  0.00              
ATOM      4  O   ASN B   3      -8.378  10.816   2.565  1.00  0.00              
ATOM      5  N   ALA B   4      -7.224  12.594   3.362  1.00  0.00              
ATOM      6  CA  ALA B   4      -7.055  13.192   2.019  1.00  0.00              
ATOM      7  C   ALA B   4      -6.222  12.321   1.079  1.00  0.00              
ATOM      8  O   ALA B   4      -6.479  12.311  -0.139  1.00  0.00              
ATOM      9  N   LYS B   5      -5.244  11.641   1.633  1.00  0.00              
ATOM     10  CA  LYS B   5      -4.388  10.764   0.795  1.00  0.00              
ATOM     11  C   LYS B   5      -5.205   9.567   0.349  1.00  0.00              
ATOM     12  O   LYS B   5      -5.108   9.075  -0.795  1.00  0.00              
ATOM     13  N   GLN B   6      -6.014   9.026   1.269  1.00  0.00              
ATOM     14  CA  GLN B   6      -6.869   7.866   0.912  1.00  0.00              
ATOM     15  C   GLN B   6      -7.846   8.272  -0.206  1.00  0.00              
ATOM     16  O   GLN B   6      -7.995   7.506  -1.179  1.00  0.00              
ATOM     17  N   GLU B   7      -8.473   9.426  -0.121  1.00  0.00              
ATOM     18  CA  GLU B   7      -9.371   9.937  -1.148  1.00  0.00              
ATOM     19  C   GLU B   7      -8.607  10.093  -2.469  1.00  0.00              
ATOM     20  O   GLU B   7      -9.132   9.636  -3.524  1.00  0.00              
ATOM     21  N   HIS B   8      -7.418  10.679  -2.411  1.00  0.00              
ATOM     22  CA  HIS B   8      -6.608  10.861  -3.636  1.00  0.00              
ATOM     23  C   HIS B   8      -6.316   9.519  -4.294  1.00  0.00              
ATOM     24  O   HIS B   8      -6.433   9.380  -5.527  1.00  0.00              
ATOM     25  N   PHE B   9      -5.939   8.494  -3.518  1.00  0.00              
ATOM     26  CA  PHE B   9      -5.641   7.186  -4.122  1.00  0.00              
ATOM     27  C   PHE B   9      -6.880   6.572  -4.786  1.00  0.00              
ATOM     28  O   PHE B   9      -6.731   5.960  -5.845  1.00  0.00              
ATOM     29  N   GLU B  10      -8.039   6.734  -4.153  1.00  0.00              
ATOM     30  CA  GLU B  10      -9.264   6.182  -4.769  1.00  0.00              
ATOM     31  C   GLU B  10      -9.496   6.884  -6.117  1.00  0.00              
ATOM     32  O   GLU B  10      -9.887   6.201  -7.097  1.00  0.00              
ATOM     33  N   LEU B  11      -9.272   8.180  -6.175  1.00  0.00              
ATOM     34  CA  LEU B  11      -9.466   8.951  -7.435  1.00  0.00              
ATOM     35  C   LEU B  11      -8.466   8.567  -8.505  1.00  0.00              
ATOM     36  O   LEU B  11      -8.792   8.426  -9.699  1.00  0.00              
ATOM     37  N   ASP B  12      -7.219   8.352  -8.047  1.00  0.00              
ATOM     38  CA  ASP B  12      -6.149   7.957  -9.003  1.00  0.00              
ATOM     39  C   ASP B  12      -6.476   6.633  -9.664  1.00  0.00              
ATOM     40  O   ASP B  12      -6.165   6.465 -10.869  1.00  0.00              
ATOM     41  N   GLN B  13      -7.038   5.660  -8.941  1.00  0.00              
ATOM     42  CA  GLN B  13      -7.392   4.393  -9.589  1.00  0.00              
ATOM     43  C   GLN B  13      -8.420   4.635 -10.719  1.00  0.00              
ATOM     44  O   GLN B  13      -8.273   4.036 -11.796  1.00  0.00              
ATOM     45  N   GLU B  14      -9.384   5.486 -10.425  1.00  0.00              
ATOM     46  CA  GLU B  14     -10.406   5.822 -11.448  1.00  0.00              
ATOM     47  C   GLU B  14      -9.758   6.450 -12.692  1.00  0.00              
ATOM     48  O   GLU B  14     -10.079   6.135 -13.843  1.00  0.00              
ATOM     49  N   TRP B  15      -8.847   7.389 -12.453  1.00  0.00              
ATOM     50  CA  TRP B  15      -8.159   8.030 -13.593  1.00  0.00              
ATOM     51  C   TRP B  15      -7.427   6.968 -14.395  1.00  0.00              
ATOM     52  O   TRP B  15      -7.542   6.936 -15.629  1.00  0.00              
ATOM     53  N   VAL B  16      -6.602   6.109 -13.741  1.00  0.00              
ATOM     54  CA  VAL B  16      -5.877   5.094 -14.499  1.00  0.00              
ATOM     55  C   VAL B  16      -6.847   4.208 -15.297  1.00  0.00              
ATOM     56  O   VAL B  16      -6.588   3.862 -16.451  1.00  0.00              
ATOM     57  N   GLU B  17      -7.926   3.773 -14.674  1.00  0.00              
ATOM     58  CA  GLU B  17      -8.908   2.926 -15.376  1.00  0.00              
ATOM     59  C   GLU B  17      -9.432   3.625 -16.629  1.00  0.00              
ATOM     60  O   GLU B  17      -9.432   3.040 -17.723  1.00  0.00              
ATOM     61  N   LEU B  18      -9.832   4.878 -16.503  1.00  0.00              
ATOM     62  CA  LEU B  18     -10.371   5.623 -17.682  1.00  0.00              
ATOM     63  C   LEU B  18      -9.307   5.896 -18.720  1.00  0.00              
ATOM     64  O   LEU B  18      -9.580   5.928 -19.960  1.00  0.00              
ATOM     65  N   MET B  19      -8.076   6.131 -18.313  1.00  0.00              
ATOM     66  CA  MET B  19      -6.996   6.337 -19.305  1.00  0.00              
ATOM     67  C   MET B  19      -6.756   5.031 -20.060  1.00  0.00              
ATOM     68  O   MET B  19      -6.510   5.126 -21.289  1.00  0.00              
ATOM     69  N   VAL B  20      -6.798   3.886 -19.401  1.00  0.00              
ATOM     70  CA  VAL B  20      -6.549   2.608 -20.101  1.00  0.00              
ATOM     71  C   VAL B  20      -7.686   2.258 -21.058  1.00  0.00              
ATOM     72  O   VAL B  20      -7.404   1.714 -22.131  1.00  0.00              
ATOM     73  N   GLU B  21      -8.856   2.636 -20.599  1.00  0.00              
ATOM     74  CA  GLU B  21     -10.071   2.357 -21.377  1.00  0.00              
ATOM     75  C   GLU B  21     -10.084   3.159 -22.678  1.00  0.00              
ATOM     76  O   GLU B  21     -10.412   2.537 -23.723  1.00  0.00              
ATOM     77  N   PRO B  29      -9.233  13.403 -22.203  1.00  0.00              
ATOM     78  CA  PRO B  29      -8.693  13.901 -20.925  1.00  0.00              
ATOM     79  C   PRO B  29      -9.552  15.048 -20.422  1.00  0.00              
ATOM     80  O   PRO B  29      -9.813  15.187 -19.221  1.00  0.00              
ATOM     81  N   GLU B  30     -10.057  15.891 -21.332  1.00  0.00              
ATOM     82  CA  GLU B  30     -10.905  17.022 -20.867  1.00  0.00              
ATOM     83  C   GLU B  30     -12.242  16.542 -20.332  1.00  0.00              
ATOM     84  O   GLU B  30     -12.769  17.070 -19.332  1.00  0.00              
ATOM     85  N   GLU B  31     -12.765  15.494 -20.954  1.00  0.00              
ATOM     86  CA  GLU B  31     -14.024  14.887 -20.487  1.00  0.00              
ATOM     87  C   GLU B  31     -13.823  14.302 -19.097  1.00  0.00              
ATOM     88  O   GLU B  31     -14.685  14.352 -18.207  1.00  0.00              
ATOM     89  N   ILE B  32     -12.649  13.705 -18.848  1.00  0.00              
ATOM     90  CA  ILE B  32     -12.332  13.124 -17.530  1.00  0.00              
ATOM     91  C   ILE B  32     -12.306  14.175 -16.433  1.00  0.00              
ATOM     92  O   ILE B  32     -12.738  13.975 -15.285  1.00  0.00              
ATOM     93  N   ARG B  33     -11.747  15.326 -16.778  1.00  0.00              
ATOM     94  CA  ARG B  33     -11.662  16.441 -15.829  1.00  0.00              
ATOM     95  C   ARG B  33     -13.089  16.844 -15.446  1.00  0.00              
ATOM     96  O   ARG B  33     -13.403  17.002 -14.271  1.00  0.00              
ATOM     97  N   LYS B  34     -13.920  16.992 -16.470  1.00  0.00              
ATOM     98  CA  LYS B  34     -15.332  17.386 -16.236  1.00  0.00              
ATOM     99  C   LYS B  34     -16.094  16.325 -15.454  1.00  0.00              
ATOM    100  O   LYS B  34     -16.851  16.671 -14.533  1.00  0.00              
ATOM    101  N   TYR B  35     -15.880  15.064 -15.752  1.00  0.00              
ATOM    102  CA  TYR B  35     -16.547  13.947 -15.091  1.00  0.00              
ATOM    103  C   TYR B  35     -16.142  13.640 -13.665  1.00  0.00              
ATOM    104  O   TYR B  35     -17.059  13.416 -12.836  1.00  0.00              
ATOM    105  N   LEU B  36     -14.856  13.582 -13.374  1.00  0.00              
ATOM    106  CA  LEU B  36     -14.381  13.262 -12.034  1.00  0.00              
ATOM    107  C   LEU B  36     -14.030  14.415 -11.106  1.00  0.00              
ATOM    108  O   LEU B  36     -13.705  14.083  -9.948  1.00  0.00              
END
