REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL009_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 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 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2ts1 
ATOM      1  N   LYS     6     -39.753  12.274 -15.345  1.00  0.00              
ATOM      2  CA  LYS     6     -39.367  11.352 -14.299  1.00  0.00              
ATOM      3  C   LYS     6     -38.271  11.927 -13.398  1.00  0.00              
ATOM      4  O   LYS     6     -38.282  11.501 -12.251  1.00  0.00              
ATOM      5  N   SER     7     -37.378  12.780 -13.908  1.00  0.00              
ATOM      6  CA  SER     7     -36.289  13.329 -13.127  1.00  0.00              
ATOM      7  C   SER     7     -36.435  14.747 -12.603  1.00  0.00              
ATOM      8  O   SER     7     -35.819  15.112 -11.576  1.00  0.00              
ATOM      9  N   GLU     8     -37.217  15.542 -13.321  1.00  0.00              
ATOM     10  CA  GLU     8     -37.362  16.940 -13.006  1.00  0.00              
ATOM     11  C   GLU     8     -37.544  17.277 -11.544  1.00  0.00              
ATOM     12  O   GLU     8     -36.847  18.235 -11.125  1.00  0.00              
ATOM     13  N   LEU     9     -38.422  16.595 -10.835  1.00  0.00              
ATOM     14  CA  LEU     9     -38.681  16.863  -9.424  1.00  0.00              
ATOM     15  C   LEU     9     -37.462  16.518  -8.572  1.00  0.00              
ATOM     16  O   LEU     9     -37.263  17.378  -7.705  1.00  0.00              
ATOM     17  N   GLN    10     -36.700  15.492  -8.785  1.00  0.00              
ATOM     18  CA  GLN    10     -35.495  15.224  -8.015  1.00  0.00              
ATOM     19  C   GLN    10     -34.431  16.296  -8.310  1.00  0.00              
ATOM     20  O   GLN    10     -33.637  16.591  -7.372  1.00  0.00              
ATOM     21  N   ALA    11     -34.366  16.795  -9.523  1.00  0.00              
ATOM     22  CA  ALA    11     -33.380  17.787  -9.936  1.00  0.00              
ATOM     23  C   ALA    11     -33.642  19.166  -9.396  1.00  0.00              
ATOM     24  O   ALA    11     -32.755  19.990  -9.183  1.00  0.00              
ATOM     25  N   LEU    12     -34.899  19.516  -9.191  1.00  0.00              
ATOM     26  CA  LEU    12     -35.312  20.810  -8.642  1.00  0.00              
ATOM     27  C   LEU    12     -34.829  20.940  -7.205  1.00  0.00              
ATOM     28  O   LEU    12     -34.388  22.020  -6.774  1.00  0.00              
ATOM     29  N   LYS    13     -34.959  19.887  -6.483  1.00  0.00              
ATOM     30  CA  LYS    13     -34.589  19.669  -5.073  1.00  0.00              
ATOM     31  C   LYS    13     -33.085  19.696  -4.847  1.00  0.00              
ATOM     32  O   LYS    13     -32.626  20.351  -3.896  1.00  0.00              
ATOM     33  N   LYS    14     -32.386  19.040  -5.741  1.00  0.00              
ATOM     34  CA  LYS    14     -30.953  18.991  -5.772  1.00  0.00              
ATOM     35  C   LYS    14     -30.197  20.245  -6.167  1.00  0.00              
ATOM     36  O   LYS    14     -29.197  20.634  -5.521  1.00  0.00              
ATOM     37  N   GLU    20     -42.412  24.195  -0.617  1.00  0.00              
ATOM     38  CA  GLU    20     -43.754  24.547  -1.094  1.00  0.00              
ATOM     39  C   GLU    20     -43.677  24.934  -2.544  1.00  0.00              
ATOM     40  O   GLU    20     -44.711  24.690  -3.199  1.00  0.00              
ATOM     41  N   GLU    21     -42.619  25.527  -3.071  1.00  0.00              
ATOM     42  CA  GLU    21     -42.587  25.844  -4.506  1.00  0.00              
ATOM     43  C   GLU    21     -42.379  24.554  -5.294  1.00  0.00              
ATOM     44  O   GLU    21     -43.057  24.222  -6.312  1.00  0.00              
ATOM     45  N   LEU    22     -41.498  23.724  -4.796  1.00  0.00              
ATOM     46  CA  LEU    22     -41.185  22.437  -5.440  1.00  0.00              
ATOM     47  C   LEU    22     -42.436  21.571  -5.463  1.00  0.00              
ATOM     48  O   LEU    22     -42.670  20.915  -6.471  1.00  0.00              
ATOM     49  N   ALA    23     -43.217  21.533  -4.401  1.00  0.00              
ATOM     50  CA  ALA    23     -44.430  20.702  -4.290  1.00  0.00              
ATOM     51  C   ALA    23     -45.508  21.091  -5.269  1.00  0.00              
ATOM     52  O   ALA    23     -46.087  20.230  -5.983  1.00  0.00              
ATOM     53  N   ALA    24     -45.723  22.391  -5.306  1.00  0.00              
ATOM     54  CA  ALA    24     -46.613  23.053  -6.220  1.00  0.00              
ATOM     55  C   ALA    24     -46.270  22.645  -7.651  1.00  0.00              
ATOM     56  O   ALA    24     -47.159  22.310  -8.439  1.00  0.00              
ATOM     57  N   LEU    25     -44.980  22.610  -8.003  1.00  0.00              
ATOM     58  CA  LEU    25     -44.515  22.224  -9.357  1.00  0.00              
ATOM     59  C   LEU    25     -44.830  20.754  -9.600  1.00  0.00              
ATOM     60  O   LEU    25     -45.149  20.322 -10.732  1.00  0.00              
ATOM     61  N   GLU    26     -44.761  19.983  -8.506  1.00  0.00              
ATOM     62  CA  GLU    26     -45.053  18.560  -8.593  1.00  0.00              
ATOM     63  C   GLU    26     -46.493  18.242  -8.997  1.00  0.00              
ATOM     64  O   GLU    26     -46.862  17.298  -9.747  1.00  0.00              
ATOM     65  N   SER    27     -47.369  19.061  -8.500  1.00  0.00              
ATOM     66  CA  SER    27     -48.829  18.984  -8.764  1.00  0.00              
ATOM     67  C   SER    27     -49.085  19.515 -10.172  1.00  0.00              
ATOM     68  O   SER    27     -49.891  18.960 -10.968  1.00  0.00              
ATOM     69  N   GLU    28     -48.368  20.544 -10.613  1.00  0.00              
ATOM     70  CA  GLU    28     -48.488  21.092 -11.964  1.00  0.00              
ATOM     71  C   GLU    28     -47.992  20.123 -13.021  1.00  0.00              
ATOM     72  O   GLU    28     -48.472  20.081 -14.168  1.00  0.00              
ATOM     73  N   LEU    29     -47.021  19.285 -12.683  1.00  0.00              
ATOM     74  CA  LEU    29     -46.441  18.254 -13.534  1.00  0.00              
ATOM     75  C   LEU    29     -47.444  17.099 -13.684  1.00  0.00              
ATOM     76  O   LEU    29     -47.479  16.414 -14.713  1.00  0.00              
ATOM     77  N   GLN    30     -48.196  16.888 -12.638  1.00  0.00              
ATOM     78  CA  GLN    30     -49.225  15.866 -12.593  1.00  0.00              
ATOM     79  C   GLN    30     -50.357  16.244 -13.546  1.00  0.00              
ATOM     80  O   GLN    30     -50.764  15.452 -14.401  1.00  0.00              
ATOM     81  N   LEU    32     -42.118  22.734 -14.719  1.00  0.00              
ATOM     82  CA  LEU    32     -41.043  22.221 -13.831  1.00  0.00              
ATOM     83  C   LEU    32     -39.716  22.292 -14.614  1.00  0.00              
ATOM     84  O   LEU    32     -38.723  22.779 -14.075  1.00  0.00              
ATOM     85  N   GLU    33     -39.740  21.878 -15.876  1.00  0.00              
ATOM     86  CA  GLU    33     -38.590  21.930 -16.779  1.00  0.00              
ATOM     87  C   GLU    33     -38.127  23.350 -17.082  1.00  0.00              
ATOM     88  O   GLU    33     -36.861  23.543 -17.173  1.00  0.00              
ATOM     89  N   LYS    34     -39.002  24.342 -17.245  1.00  0.00              
ATOM     90  CA  LYS    34     -38.463  25.700 -17.524  1.00  0.00              
ATOM     91  C   LYS    34     -37.889  26.332 -16.256  1.00  0.00              
ATOM     92  O   LYS    34     -36.823  26.996 -16.363  1.00  0.00              
ATOM     93  N   LYS    35     -38.548  26.140 -15.130  1.00  0.00              
ATOM     94  CA  LYS    35     -38.130  26.663 -13.815  1.00  0.00              
ATOM     95  C   LYS    35     -36.741  26.114 -13.443  1.00  0.00              
ATOM     96  O   LYS    35     -35.914  26.851 -12.881  1.00  0.00              
ATOM     97  N   LEU    36     -36.542  24.821 -13.719  1.00  0.00              
ATOM     98  CA  LEU    36     -35.225  24.253 -13.430  1.00  0.00              
ATOM     99  C   LEU    36     -34.155  24.936 -14.295  1.00  0.00              
ATOM    100  O   LEU    36     -33.171  25.510 -13.808  1.00  0.00              
ATOM    101  N   ALA    37     -34.428  24.928 -15.609  1.00  0.00              
ATOM    102  CA  ALA    37     -33.565  25.535 -16.619  1.00  0.00              
ATOM    103  C   ALA    37     -33.222  26.973 -16.331  1.00  0.00              
ATOM    104  O   ALA    37     -32.041  27.309 -16.543  1.00  0.00              
ATOM    105  N   ALA    38     -34.181  27.793 -15.929  1.00  0.00              
ATOM    106  CA  ALA    38     -33.937  29.206 -15.594  1.00  0.00              
ATOM    107  C   ALA    38     -33.098  29.427 -14.341  1.00  0.00              
ATOM    108  O   ALA    38     -32.139  30.208 -14.338  1.00  0.00              
ATOM    109  N   LEU    39     -33.440  28.716 -13.290  1.00  0.00              
ATOM    110  CA  LEU    39     -32.838  28.710 -11.970  1.00  0.00              
ATOM    111  C   LEU    39     -31.365  28.353 -12.035  1.00  0.00              
ATOM    112  O   LEU    39     -30.508  29.102 -11.592  1.00  0.00              
ATOM    113  N   LYS    40     -31.109  27.198 -12.638  1.00  0.00              
ATOM    114  CA  LYS    40     -29.739  26.682 -12.787  1.00  0.00              
ATOM    115  C   LYS    40     -28.940  27.528 -13.755  1.00  0.00              
ATOM    116  O   LYS    40     -27.810  27.875 -13.354  1.00  0.00              
ATOM    117  N   SER    41     -29.457  27.939 -14.898  1.00  0.00              
ATOM    118  CA  SER    41     -28.703  28.820 -15.797  1.00  0.00              
ATOM    119  C   SER    41     -28.332  30.164 -15.176  1.00  0.00              
ATOM    120  O   SER    41     -27.201  30.682 -15.442  1.00  0.00              
ATOM    121  N   LYS    42     -29.198  30.729 -14.387  1.00  0.00              
ATOM    122  CA  LYS    42     -28.982  31.986 -13.687  1.00  0.00              
ATOM    123  C   LYS    42     -27.864  31.817 -12.656  1.00  0.00              
ATOM    124  O   LYS    42     -26.947  32.613 -12.439  1.00  0.00              
ATOM    125  N   LEU    43     -27.941  30.701 -11.926  1.00  0.00              
ATOM    126  CA  LEU    43     -26.989  30.354 -10.892  1.00  0.00              
ATOM    127  C   LEU    43     -25.591  30.394 -11.490  1.00  0.00              
ATOM    128  O   LEU    43     -24.727  31.118 -11.026  1.00  0.00              
ATOM    129  N   GLN    44     -25.435  29.579 -12.495  1.00  0.00              
ATOM    130  CA  GLN    44     -24.185  29.380 -13.194  1.00  0.00              
ATOM    131  C   GLN    44     -23.741  30.463 -14.127  1.00  0.00              
ATOM    132  O   GLN    44     -22.532  30.799 -14.132  1.00  0.00              
END
