REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL009_4_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0073  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0073, DSD, synthetic  
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 The two segments aligned with 1cos_A and 1cos_C, respectively, should  
METHOD not be evaluated as two independent segments, rather 1cos_A and 1cos_C  
METHOD should be considered as parts of one integral object, i.e., the relative  
METHOD spatial relationship between residues of 1cos_A and 1cos_C should be  
METHOD kept.  
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 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1cos_A 
ATOM      1  N   LEU    22       0.800 -28.015  25.074  1.00  0.00              
ATOM      2  CA  LEU    22       0.045 -27.649  23.874  1.00  0.00              
ATOM      3  C   LEU    22      -0.264 -26.184  23.771  1.00  0.00              
ATOM      4  O   LEU    22      -0.183 -25.585  22.710  1.00  0.00              
ATOM      5  N   ALA    23      -0.412 -25.566  24.920  1.00  0.00              
ATOM      6  CA  ALA    23      -0.520 -24.140  24.981  1.00  0.00              
ATOM      7  C   ALA    23       0.818 -23.572  24.744  1.00  0.00              
ATOM      8  O   ALA    23       0.965 -22.425  24.381  1.00  0.00              
ATOM      9  N   ALA    24       1.815 -24.268  25.213  1.00  0.00              
ATOM     10  CA  ALA    24       3.113 -23.651  25.038  1.00  0.00              
ATOM     11  C   ALA    24       3.406 -23.533  23.572  1.00  0.00              
ATOM     12  O   ALA    24       3.888 -22.498  23.127  1.00  0.00              
ATOM     13  N   LEU    25       3.054 -24.583  22.815  1.00  0.00              
ATOM     14  CA  LEU    25       3.257 -24.589  21.351  1.00  0.00              
ATOM     15  C   LEU    25       2.548 -23.421  20.659  1.00  0.00              
ATOM     16  O   LEU    25       3.079 -22.778  19.739  1.00  0.00              
ATOM     17  N   GLU    26       1.317 -23.179  21.118  1.00  0.00              
ATOM     18  CA  GLU    26       0.498 -22.073  20.684  1.00  0.00              
ATOM     19  C   GLU    26       1.144 -20.737  20.920  1.00  0.00              
ATOM     20  O   GLU    26       0.913 -19.830  20.120  1.00  0.00              
ATOM     21  N   SER    27       1.898 -20.573  22.015  1.00  0.00              
ATOM     22  CA  SER    27       2.490 -19.260  22.250  1.00  0.00              
ATOM     23  C   SER    27       3.770 -19.108  21.454  1.00  0.00              
ATOM     24  O   SER    27       4.197 -18.040  21.014  1.00  0.00              
ATOM     25  N   GLU    28       4.462 -20.219  21.334  1.00  0.00              
ATOM     26  CA  GLU    28       5.627 -20.150  20.535  1.00  0.00              
ATOM     27  C   GLU    28       5.206 -19.801  19.088  1.00  0.00              
ATOM     28  O   GLU    28       5.854 -18.962  18.448  1.00  0.00              
ATOM     29  N   LEU    29       4.044 -20.299  18.585  1.00  0.00              
ATOM     30  CA  LEU    29       3.579 -19.918  17.215  1.00  0.00              
ATOM     31  C   LEU    29       3.240 -18.416  17.008  1.00  0.00              
ATOM     32  O   LEU    29       3.650 -17.763  16.079  1.00  0.00              
ATOM     33  N   GLN    30       2.533 -17.833  17.932  1.00  0.00              
ATOM     34  CA  GLN    30       2.149 -16.440  17.876  1.00  0.00              
ATOM     35  C   GLN    30       3.360 -15.591  17.899  1.00  0.00              
ATOM     36  O   GLN    30       3.380 -14.526  17.316  1.00  0.00              
ATOM     37  N   ALA    31       4.286 -15.976  18.727  1.00  0.00              
ATOM     38  CA  ALA    31       5.525 -15.222  18.778  1.00  0.00              
ATOM     39  C   ALA    31       6.400 -15.298  17.467  1.00  0.00              
ATOM     40  O   ALA    31       7.135 -14.371  17.133  1.00  0.00              
ATOM     41  N   LEU    32       6.416 -16.415  16.720  1.00  0.00              
ATOM     42  CA  LEU    32       7.146 -16.438  15.453  1.00  0.00              
ATOM     43  C   LEU    32       6.355 -15.717  14.333  1.00  0.00              
ATOM     44  O   LEU    32       6.931 -14.895  13.675  1.00  0.00              
ATOM     45  N   GLU    33       5.011 -15.820  14.282  1.00  0.00              
ATOM     46  CA  GLU    33       4.124 -15.005  13.446  1.00  0.00              
ATOM     47  C   GLU    33       4.331 -13.511  13.642  1.00  0.00              
ATOM     48  O   GLU    33       4.328 -12.662  12.741  1.00  0.00              
ATOM     49  N   LYS    34       4.261 -13.155  14.897  1.00  0.00              
ATOM     50  CA  LYS    34       4.396 -11.785  15.252  1.00  0.00              
ATOM     51  C   LYS    34       5.693 -11.251  14.792  1.00  0.00              
ATOM     52  O   LYS    34       5.765 -10.070  14.457  1.00  0.00              
ATOM     53  N   LYS    35       6.721 -12.086  14.926  1.00  0.00              
ATOM     54  CA  LYS    35       8.078 -11.693  14.574  1.00  0.00              
ATOM     55  C   LYS    35       8.345 -11.618  13.068  1.00  0.00              
ATOM     56  O   LYS    35       8.963 -10.655  12.580  1.00  0.00              
ATOM     57  N   LEU    36       7.748 -12.569  12.348  1.00  0.00              
ATOM     58  CA  LEU    36       7.734 -12.579  10.912  1.00  0.00              
ATOM     59  C   LEU    36       7.142 -11.265  10.388  1.00  0.00              
ATOM     60  O   LEU    36       7.579 -10.680   9.386  1.00  0.00              
ATOM     61  N   ALA    37       6.103 -10.820  11.055  1.00  0.00              
ATOM     62  CA  ALA    37       5.432  -9.627  10.657  1.00  0.00              
ATOM     63  C   ALA    37       6.213  -8.373  10.988  1.00  0.00              
ATOM     64  O   ALA    37       6.094  -7.328  10.337  1.00  0.00              
ATOM     65  N   ALA    38       7.004  -8.463  12.043  1.00  0.00              
ATOM     66  CA  ALA    38       7.845  -7.329  12.371  1.00  0.00              
ATOM     67  C   ALA    38       9.049  -7.291  11.412  1.00  0.00              
ATOM     68  O   ALA    38       9.487  -6.239  10.960  1.00  0.00              
ATOM     69  N   LEU    39       9.525  -8.444  11.002  1.00  0.00              
ATOM     70  CA  LEU    39      10.568  -8.446   9.999  1.00  0.00              
ATOM     71  C   LEU    39      10.103  -7.790   8.712  1.00  0.00              
ATOM     72  O   LEU    39      10.926  -7.194   8.029  1.00  0.00              
ATOM     73  N   LYS    40       8.806  -7.938   8.369  1.00  0.00              
ATOM     74  CA  LYS    40       8.238  -7.450   7.099  1.00  0.00              
ATOM     75  C   LYS    40       8.138  -5.956   7.054  1.00  0.00              
ATOM     76  O   LYS    40       8.485  -5.297   6.074  1.00  0.00              
ATOM     77  N   SER    41       7.740  -5.383   8.173  1.00  0.00              
ATOM     78  CA  SER    41       7.704  -3.944   8.262  1.00  0.00              
ATOM     79  C   SER    41       9.172  -3.370   8.325  1.00  0.00              
ATOM     80  O   SER    41       9.404  -2.191   8.102  1.00  0.00              
ATOM     81  N   LYS    42      10.171  -4.203   8.653  1.00  0.00              
ATOM     82  CA  LYS    42      11.614  -3.891   8.625  1.00  0.00              
ATOM     83  C   LYS    42      12.191  -3.864   7.172  1.00  0.00              
ATOM     84  O   LYS    42      12.781  -2.862   6.752  1.00  0.00              
ATOM     85  N   LEU    43      11.931  -4.953   6.397  1.00  0.00              
ATOM     86  CA  LEU    43      12.249  -5.092   4.982  1.00  0.00              
ATOM     87  C   LEU    43      11.685  -3.903   4.275  1.00  0.00              
ATOM     88  O   LEU    43      12.448  -3.048   3.849  1.00  0.00              
ATOM     89  N   GLN    44      10.380  -3.713   4.459  1.00  0.00              
ATOM     90  CA  GLN    44       9.620  -2.549   3.990  1.00  0.00              
ATOM     91  C   GLN    44      10.236  -1.144   4.283  1.00  0.00              
ATOM     92  O   GLN    44       9.959  -0.132   3.586  1.00  0.00              
ATOM     93  N   ALA    45      10.992  -1.037   5.387  1.00  0.00              
ATOM     94  CA  ALA    45      11.610   0.225   5.759  1.00  0.00              
ATOM     95  C   ALA    45      12.787   0.449   4.882  1.00  0.00              
ATOM     96  O   ALA    45      13.175   1.566   4.618  1.00  0.00              
ATOM     97  N   LEU    46      13.406  -0.673   4.575  1.00  0.00              
ATOM     98  CA  LEU    46      14.630  -0.744   3.827  1.00  0.00              
ATOM     99  C   LEU    46      14.400  -0.466   2.381  1.00  0.00              
ATOM    100  O   LEU    46      15.198   0.171   1.725  1.00  0.00              
ATOM    101  N   LYS    47      13.315  -0.982   1.877  1.00  0.00              
ATOM    102  CA  LYS    47      13.022  -0.810   0.491  1.00  0.00              
ATOM    103  C   LYS    47      12.550   0.600   0.274  1.00  0.00              
ATOM    104  O   LYS    47      13.047   1.345  -0.543  1.00  0.00              
ATOM    105  N   GLY    48      11.560   0.951   1.048  1.00  0.00              
ATOM    106  CA  GLY    48      10.892   2.209   0.916  1.00  0.00              
ATOM    107  C   GLY    48      11.833   3.366   1.234  1.00  0.00              
ATOM    108  O   GLY    48      11.707   4.169   2.158  1.00  0.00              
END
