REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0084AL009_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0084  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0084, RLZ  
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: 1t7p_A 
ATOM      1  N   GLU     5      25.896  36.704  10.714  1.00  0.00              
ATOM      2  CA  GLU     5      25.905  35.465  11.494  1.00  0.00              
ATOM      3  C   GLU     5      24.711  34.577  11.146  1.00  0.00              
ATOM      4  O   GLU     5      24.765  33.358  11.314  1.00  0.00              
ATOM      5  N   GLY     6      23.641  35.202  10.656  1.00  0.00              
ATOM      6  CA  GLY     6      22.413  34.496  10.282  1.00  0.00              
ATOM      7  C   GLY     6      22.689  33.591   9.084  1.00  0.00              
ATOM      8  O   GLY     6      22.379  32.395   9.104  1.00  0.00              
ATOM      9  N   VAL     7      23.283  34.181   8.048  1.00  0.00              
ATOM     10  CA  VAL     7      23.626  33.466   6.824  1.00  0.00              
ATOM     11  C   VAL     7      24.706  32.447   7.157  1.00  0.00              
ATOM     12  O   VAL     7      24.774  31.384   6.542  1.00  0.00              
ATOM     13  N   LEU     8      25.532  32.785   8.150  1.00  0.00              
ATOM     14  CA  LEU     8      26.606  31.910   8.591  1.00  0.00              
ATOM     15  C   LEU     8      26.064  30.582   9.082  1.00  0.00              
ATOM     16  O   LEU     8      26.530  29.533   8.634  1.00  0.00              
ATOM     17  N   LYS     9      25.071  30.626   9.977  1.00  0.00              
ATOM     18  CA  LYS     9      24.450  29.412  10.521  1.00  0.00              
ATOM     19  C   LYS     9      23.808  28.581   9.419  1.00  0.00              
ATOM     20  O   LYS     9      23.928  27.357   9.409  1.00  0.00              
ATOM     21  N   LYS    10      23.104  29.261   8.513  1.00  0.00              
ATOM     22  CA  LYS    10      22.427  28.607   7.395  1.00  0.00              
ATOM     23  C   LYS    10      23.404  27.789   6.559  1.00  0.00              
ATOM     24  O   LYS    10      23.182  26.605   6.324  1.00  0.00              
ATOM     25  N   LEU    11      24.491  28.432   6.140  1.00  0.00              
ATOM     26  CA  LEU    11      25.525  27.804   5.325  1.00  0.00              
ATOM     27  C   LEU    11      26.258  26.663   6.038  1.00  0.00              
ATOM     28  O   LEU    11      26.578  25.643   5.423  1.00  0.00              
ATOM     29  N   ARG    12      26.506  26.839   7.334  1.00  0.00              
ATOM     30  CA  ARG    12      27.193  25.837   8.140  1.00  0.00              
ATOM     31  C   ARG    12      26.390  24.544   8.243  1.00  0.00              
ATOM     32  O   ARG    12      26.912  23.465   7.967  1.00  0.00              
ATOM     33  N   ALA    13      25.119  24.661   8.625  1.00  0.00              
ATOM     34  CA  ALA    13      24.249  23.495   8.775  1.00  0.00              
ATOM     35  C   ALA    13      23.817  22.894   7.439  1.00  0.00              
ATOM     36  O   ALA    13      23.492  21.710   7.363  1.00  0.00              
ATOM     37  N   VAL    14      23.823  23.720   6.394  1.00  0.00              
ATOM     38  CA  VAL    14      23.442  23.301   5.050  1.00  0.00              
ATOM     39  C   VAL    14      24.499  22.320   4.514  1.00  0.00              
ATOM     40  O   VAL    14      24.162  21.251   3.996  1.00  0.00              
ATOM     41  N   GLU    15      25.774  22.678   4.675  1.00  0.00              
ATOM     42  CA  GLU    15      26.880  21.843   4.211  1.00  0.00              
ATOM     43  C   GLU    15      27.236  20.682   5.140  1.00  0.00              
ATOM     44  O   GLU    15      27.708  19.634   4.682  1.00  0.00              
ATOM     45  N   ASN    16      26.997  20.860   6.438  1.00  0.00              
ATOM     46  CA  ASN    16      27.291  19.817   7.417  1.00  0.00              
ATOM     47  C   ASN    16      26.210  18.728   7.402  1.00  0.00              
ATOM     48  O   ASN    16      26.464  17.585   7.785  1.00  0.00              
ATOM     49  N   GLU    17      25.011  19.092   6.952  1.00  0.00              
ATOM     50  CA  GLU    17      23.896  18.152   6.867  1.00  0.00              
ATOM     51  C   GLU    17      24.041  17.295   5.598  1.00  0.00              
ATOM     52  O   GLU    17      23.629  16.131   5.572  1.00  0.00              
ATOM     53  N   LEU    18      24.644  17.874   4.558  1.00  0.00              
ATOM     54  CA  LEU    18      24.856  17.173   3.290  1.00  0.00              
ATOM     55  C   LEU    18      25.885  16.055   3.474  1.00  0.00              
ATOM     56  O   LEU    18      25.703  14.943   2.966  1.00  0.00              
ATOM     57  N   TYR    20      29.243  12.969   7.773  1.00  0.00              
ATOM     58  CA  TYR    20      30.408  12.183   8.169  1.00  0.00              
ATOM     59  C   TYR    20      31.532  13.105   8.644  1.00  0.00              
ATOM     60  O   TYR    20      32.537  12.638   9.191  1.00  0.00              
ATOM     61  N   ASN    21      31.375  14.409   8.406  1.00  0.00              
ATOM     62  CA  ASN    21      32.371  15.382   8.841  1.00  0.00              
ATOM     63  C   ASN    21      32.358  15.404  10.364  1.00  0.00              
ATOM     64  O   ASN    21      33.414  15.455  10.989  1.00  0.00              
ATOM     65  N   LYS    22      31.158  15.344  10.946  1.00  0.00              
ATOM     66  CA  LYS    22      30.977  15.334  12.402  1.00  0.00              
ATOM     67  C   LYS    22      31.583  14.070  13.033  1.00  0.00              
ATOM     68  O   LYS    22      32.269  14.142  14.046  1.00  0.00              
ATOM     69  N   SER    23      31.323  12.920  12.421  1.00  0.00              
ATOM     70  CA  SER    23      31.851  11.640  12.897  1.00  0.00              
ATOM     71  C   SER    23      33.379  11.623  12.823  1.00  0.00              
ATOM     72  O   SER    23      34.043  11.076  13.703  1.00  0.00              
ATOM     73  N   LEU    24      33.933  12.224  11.770  1.00  0.00              
ATOM     74  CA  LEU    24      35.388  12.276  11.597  1.00  0.00              
ATOM     75  C   LEU    24      36.031  13.140  12.676  1.00  0.00              
ATOM     76  O   LEU    24      37.039  12.750  13.261  1.00  0.00              
ATOM     77  N   LEU    25      35.439  14.305  12.932  1.00  0.00              
ATOM     78  CA  LEU    25      35.936  15.233  13.950  1.00  0.00              
ATOM     79  C   LEU    25      35.929  14.588  15.339  1.00  0.00              
ATOM     80  O   LEU    25      36.897  14.696  16.096  1.00  0.00              
ATOM     81  N   GLU    26      34.830  13.905  15.650  1.00  0.00              
ATOM     82  CA  GLU    26      34.662  13.239  16.937  1.00  0.00              
ATOM     83  C   GLU    26      35.680  12.133  17.189  1.00  0.00              
ATOM     84  O   GLU    26      36.234  12.044  18.286  1.00  0.00              
ATOM     85  N   GLU    27      35.945  11.313  16.173  1.00  0.00              
ATOM     86  CA  GLU    27      36.907  10.226  16.314  1.00  0.00              
ATOM     87  C   GLU    27      38.303  10.787  16.551  1.00  0.00              
ATOM     88  O   GLU    27      39.091  10.196  17.289  1.00  0.00              
ATOM     89  N   VAL    28      38.589  11.941  15.942  1.00  0.00              
ATOM     90  CA  VAL    28      39.885  12.606  16.094  1.00  0.00              
ATOM     91  C   VAL    28      40.028  13.038  17.552  1.00  0.00              
ATOM     92  O   VAL    28      41.090  12.873  18.148  1.00  0.00              
ATOM     93  N   LYS    29      38.940  13.568  18.116  1.00  0.00              
ATOM     94  CA  LYS    29      38.904  14.026  19.508  1.00  0.00              
ATOM     95  C   LYS    29      39.079  12.899  20.510  1.00  0.00              
ATOM     96  O   LYS    29      39.813  13.041  21.486  1.00  0.00              
ATOM     97  N   ASP    30      38.385  11.788  20.273  1.00  0.00              
ATOM     98  CA  ASP    30      38.458  10.623  21.149  1.00  0.00              
ATOM     99  C   ASP    30      39.872  10.036  21.115  1.00  0.00              
ATOM    100  O   ASP    30      40.325   9.435  22.082  1.00  0.00              
ATOM    101  N   GLU    31      40.566  10.234  20.000  1.00  0.00              
ATOM    102  CA  GLU    31      41.925   9.735  19.828  1.00  0.00              
ATOM    103  C   GLU    31      42.971  10.667  20.460  1.00  0.00              
ATOM    104  O   GLU    31      43.968  10.204  21.018  1.00  0.00              
ATOM    105  N   LEU    32      42.719  11.972  20.406  1.00  0.00              
ATOM    106  CA  LEU    32      43.665  12.945  20.935  1.00  0.00              
ATOM    107  C   LEU    32      43.436  13.508  22.339  1.00  0.00              
ATOM    108  O   LEU    32      44.399  13.709  23.069  1.00  0.00              
END
