REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL009_5 
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  5   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1au7_A 
ATOM      1  N   ALA     3       4.922  12.591  34.476  1.00  0.00              
ATOM      2  CA  ALA     3       4.195  13.846  34.417  1.00  0.00              
ATOM      3  C   ALA     3       2.692  13.636  34.629  1.00  0.00              
ATOM      4  O   ALA     3       2.006  14.500  35.172  1.00  0.00              
ATOM      5  N   ALA     4       2.199  12.464  34.241  1.00  0.00              
ATOM      6  CA  ALA     4       0.782  12.122  34.374  1.00  0.00              
ATOM      7  C   ALA     4       0.519  11.702  35.820  1.00  0.00              
ATOM      8  O   ALA     4      -0.466  12.109  36.423  1.00  0.00              
ATOM      9  N   LEU     5       1.427  10.909  36.381  1.00  0.00              
ATOM     10  CA  LEU     5       1.342  10.471  37.769  1.00  0.00              
ATOM     11  C   LEU     5       1.292  11.697  38.669  1.00  0.00              
ATOM     12  O   LEU     5       0.462  11.772  39.568  1.00  0.00              
ATOM     13  N   LYS     6       2.185  12.649  38.421  1.00  0.00              
ATOM     14  CA  LYS     6       2.244  13.882  39.179  1.00  0.00              
ATOM     15  C   LYS     6       0.989  14.714  39.008  1.00  0.00              
ATOM     16  O   LYS     6       0.628  15.490  39.897  1.00  0.00              
ATOM     17  N   SER     7       0.356  14.612  37.840  1.00  0.00              
ATOM     18  CA  SER     7      -0.854  15.382  37.563  1.00  0.00              
ATOM     19  C   SER     7      -2.000  14.859  38.436  1.00  0.00              
ATOM     20  O   SER     7      -2.653  15.618  39.167  1.00  0.00              
ATOM     21  N   GLU     8      -2.211  13.551  38.403  1.00  0.00              
ATOM     22  CA  GLU     8      -3.220  12.940  39.231  1.00  0.00              
ATOM     23  C   GLU     8      -2.896  13.248  40.703  1.00  0.00              
ATOM     24  O   GLU     8      -3.763  13.762  41.443  1.00  0.00              
ATOM     25  N   LEU     9      -1.653  12.972  41.131  1.00  0.00              
ATOM     26  CA  LEU     9      -1.262  13.204  42.527  1.00  0.00              
ATOM     27  C   LEU     9      -1.700  14.547  43.071  1.00  0.00              
ATOM     28  O   LEU     9      -2.414  14.593  44.065  1.00  0.00              
ATOM     29  N   GLN    10      -1.356  15.637  42.408  1.00  0.00              
ATOM     30  CA  GLN    10      -1.778  16.930  42.935  1.00  0.00              
ATOM     31  C   GLN    10      -3.230  17.304  42.727  1.00  0.00              
ATOM     32  O   GLN    10      -3.693  18.321  43.237  1.00  0.00              
ATOM     33  N   ALA    11      -3.967  16.516  41.967  1.00  0.00              
ATOM     34  CA  ALA    11      -5.383  16.822  41.831  1.00  0.00              
ATOM     35  C   ALA    11      -5.965  16.298  43.135  1.00  0.00              
ATOM     36  O   ALA    11      -6.687  16.995  43.857  1.00  0.00              
ATOM     37  N   LEU    12      -5.606  15.058  43.440  1.00  0.00              
ATOM     38  CA  LEU    12      -6.024  14.436  44.675  1.00  0.00              
ATOM     39  C   LEU    12      -5.597  15.273  45.899  1.00  0.00              
ATOM     40  O   LEU    12      -6.400  15.534  46.790  1.00  0.00              
ATOM     41  N   LYS    13      -4.370  15.766  45.906  1.00  0.00              
ATOM     42  CA  LYS    13      -3.906  16.586  47.003  1.00  0.00              
ATOM     43  C   LYS    13      -4.912  17.701  47.277  1.00  0.00              
ATOM     44  O   LYS    13      -5.323  17.924  48.421  1.00  0.00              
ATOM     45  N   LYS    14      -5.296  18.419  46.227  1.00  0.00              
ATOM     46  CA  LYS    14      -6.256  19.508  46.380  1.00  0.00              
ATOM     47  C   LYS    14      -7.673  19.087  46.794  1.00  0.00              
ATOM     48  O   LYS    14      -8.484  19.915  47.177  1.00  0.00              
ATOM     49  N   GLU    15      -8.005  17.821  46.638  1.00  0.00              
ATOM     50  CA  GLU    15      -9.312  17.388  47.041  1.00  0.00              
ATOM     51  C   GLU    15      -9.301  17.006  48.504  1.00  0.00              
ATOM     52  O   GLU    15     -10.201  17.371  49.260  1.00  0.00              
ATOM     53  N   PRO    19      -4.978   5.546  54.632  1.00  0.00              
ATOM     54  CA  PRO    19      -4.075   4.475  54.236  1.00  0.00              
ATOM     55  C   PRO    19      -4.681   3.577  53.133  1.00  0.00              
ATOM     56  O   PRO    19      -3.960   2.859  52.425  1.00  0.00              
ATOM     57  N   GLU    20      -5.997   3.671  52.951  1.00  0.00              
ATOM     58  CA  GLU    20      -6.703   2.868  51.955  1.00  0.00              
ATOM     59  C   GLU    20      -6.552   3.616  50.636  1.00  0.00              
ATOM     60  O   GLU    20      -6.177   3.042  49.610  1.00  0.00              
ATOM     61  N   GLU    21      -6.835   4.911  50.699  1.00  0.00              
ATOM     62  CA  GLU    21      -6.733   5.812  49.566  1.00  0.00              
ATOM     63  C   GLU    21      -5.309   5.753  48.974  1.00  0.00              
ATOM     64  O   GLU    21      -5.127   5.581  47.754  1.00  0.00              
ATOM     65  N   LEU    22      -4.294   5.900  49.835  1.00  0.00              
ATOM     66  CA  LEU    22      -2.894   5.887  49.387  1.00  0.00              
ATOM     67  C   LEU    22      -2.581   4.586  48.685  1.00  0.00              
ATOM     68  O   LEU    22      -1.929   4.561  47.643  1.00  0.00              
ATOM     69  N   ALA    23      -3.137   3.515  49.229  1.00  0.00              
ATOM     70  CA  ALA    23      -2.948   2.172  48.701  1.00  0.00              
ATOM     71  C   ALA    23      -3.655   1.996  47.354  1.00  0.00              
ATOM     72  O   ALA    23      -3.265   1.162  46.532  1.00  0.00              
ATOM     73  N   ALA    24      -4.719   2.762  47.147  1.00  0.00              
ATOM     74  CA  ALA    24      -5.493   2.714  45.918  1.00  0.00              
ATOM     75  C   ALA    24      -4.781   3.501  44.816  1.00  0.00              
ATOM     76  O   ALA    24      -4.615   2.983  43.717  1.00  0.00              
ATOM     77  N   LEU    25      -4.366   4.738  45.101  1.00  0.00              
ATOM     78  CA  LEU    25      -3.616   5.569  44.146  1.00  0.00              
ATOM     79  C   LEU    25      -2.303   4.867  43.694  1.00  0.00              
ATOM     80  O   LEU    25      -1.758   5.125  42.622  1.00  0.00              
ATOM     81  N   GLU    26      -1.772   4.014  44.549  1.00  0.00              
ATOM     82  CA  GLU    26      -0.557   3.280  44.266  1.00  0.00              
ATOM     83  C   GLU    26      -0.880   2.193  43.265  1.00  0.00              
ATOM     84  O   GLU    26      -0.136   2.004  42.304  1.00  0.00              
ATOM     85  N   SER    27      -1.948   1.450  43.512  1.00  0.00              
ATOM     86  CA  SER    27      -2.356   0.393  42.610  1.00  0.00              
ATOM     87  C   SER    27      -2.768   1.014  41.270  1.00  0.00              
ATOM     88  O   SER    27      -2.426   0.502  40.229  1.00  0.00              
ATOM     89  N   GLU    28      -3.414   2.169  41.316  1.00  0.00              
ATOM     90  CA  GLU    28      -3.862   2.883  40.132  1.00  0.00              
ATOM     91  C   GLU    28      -2.730   3.408  39.227  1.00  0.00              
ATOM     92  O   GLU    28      -2.906   3.527  37.993  1.00  0.00              
ATOM     93  N   LEU    29      -1.618   3.815  39.846  1.00  0.00              
ATOM     94  CA  LEU    29      -0.473   4.357  39.116  1.00  0.00              
ATOM     95  C   LEU    29       0.717   3.385  39.032  1.00  0.00              
ATOM     96  O   LEU    29       1.729   3.667  38.372  1.00  0.00              
ATOM     97  N   LEU    32       3.232   1.727  47.540  1.00  0.00              
ATOM     98  CA  LEU    32       2.470   2.506  48.518  1.00  0.00              
ATOM     99  C   LEU    32       3.367   3.533  49.255  1.00  0.00              
ATOM    100  O   LEU    32       2.969   4.681  49.494  1.00  0.00              
ATOM    101  N   GLU    33       4.630   3.163  49.456  1.00  0.00              
ATOM    102  CA  GLU    33       5.585   4.023  50.156  1.00  0.00              
ATOM    103  C   GLU    33       5.944   5.297  49.411  1.00  0.00              
ATOM    104  O   GLU    33       6.152   6.356  50.018  1.00  0.00              
ATOM    105  N   LYS    34       5.929   5.202  48.089  1.00  0.00              
ATOM    106  CA  LYS    34       6.243   6.322  47.219  1.00  0.00              
ATOM    107  C   LYS    34       5.130   7.360  47.283  1.00  0.00              
ATOM    108  O   LYS    34       5.392   8.563  47.354  1.00  0.00              
ATOM    109  N   LYS    35       3.883   6.879  47.319  1.00  0.00              
ATOM    110  CA  LYS    35       2.719   7.774  47.383  1.00  0.00              
ATOM    111  C   LYS    35       2.708   8.414  48.756  1.00  0.00              
ATOM    112  O   LYS    35       2.491   9.622  48.871  1.00  0.00              
ATOM    113  N   LEU    36       2.956   7.605  49.793  1.00  0.00              
ATOM    114  CA  LEU    36       3.021   8.089  51.176  1.00  0.00              
ATOM    115  C   LEU    36       3.990   9.270  51.345  1.00  0.00              
ATOM    116  O   LEU    36       3.604  10.347  51.848  1.00  0.00              
ATOM    117  N   ALA    37       5.255   9.071  50.948  1.00  0.00              
ATOM    118  CA  ALA    37       6.267  10.131  51.026  1.00  0.00              
ATOM    119  C   ALA    37       6.013  11.331  50.117  1.00  0.00              
ATOM    120  O   ALA    37       6.419  12.481  50.410  1.00  0.00              
ATOM    121  N   ALA    38       5.360  11.078  48.991  1.00  0.00              
ATOM    122  CA  ALA    38       5.069  12.147  48.085  1.00  0.00              
ATOM    123  C   ALA    38       4.095  13.101  48.753  1.00  0.00              
ATOM    124  O   ALA    38       4.216  14.326  48.635  1.00  0.00              
ATOM    125  N   LEU    39       3.131  12.552  49.483  1.00  0.00              
ATOM    126  CA  LEU    39       2.163  13.398  50.171  1.00  0.00              
ATOM    127  C   LEU    39       2.809  14.177  51.276  1.00  0.00              
ATOM    128  O   LEU    39       2.595  15.396  51.394  1.00  0.00              
ATOM    129  N   LYS    40       3.605  13.491  52.102  1.00  0.00              
ATOM    130  CA  LYS    40       4.276  14.158  53.233  1.00  0.00              
ATOM    131  C   LYS    40       5.113  15.347  52.777  1.00  0.00              
ATOM    132  O   LYS    40       4.983  16.447  53.332  1.00  0.00              
ATOM    133  N   SER    41       5.968  15.153  51.769  1.00  0.00              
ATOM    134  CA  SER    41       6.797  16.243  51.269  1.00  0.00              
ATOM    135  C   SER    41       6.038  17.450  50.773  1.00  0.00              
ATOM    136  O   SER    41       6.469  18.607  50.931  1.00  0.00              
ATOM    137  N   LYS    42       4.932  17.171  50.110  1.00  0.00              
ATOM    138  CA  LYS    42       4.049  18.183  49.552  1.00  0.00              
ATOM    139  C   LYS    42       3.441  19.019  50.691  1.00  0.00              
ATOM    140  O   LYS    42       3.304  20.239  50.579  1.00  0.00              
ATOM    141  N   LEU    43       3.024  18.350  51.767  1.00  0.00              
ATOM    142  CA  LEU    43       2.499  19.054  52.966  1.00  0.00              
ATOM    143  C   LEU    43       3.618  19.884  53.611  1.00  0.00              
ATOM    144  O   LEU    43       3.413  21.065  53.954  1.00  0.00              
ATOM    145  N   GLN    44       4.797  19.263  53.764  1.00  0.00              
ATOM    146  CA  GLN    44       5.987  19.906  54.345  1.00  0.00              
ATOM    147  C   GLN    44       6.462  21.150  53.615  1.00  0.00              
ATOM    148  O   GLN    44       6.789  22.148  54.228  1.00  0.00              
ATOM    149  N   ALA    45       6.477  21.102  52.301  1.00  0.00              
ATOM    150  CA  ALA    45       6.691  22.467  51.655  1.00  0.00              
ATOM    151  C   ALA    45       5.793  23.642  51.985  1.00  0.00              
ATOM    152  O   ALA    45       6.254  24.778  51.986  1.00  0.00              
END
