REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0084AL009_1 
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  1 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1uby 
ATOM      1  N   GLU     5      -1.641  27.575  74.201  1.00  0.00              
ATOM      2  CA  GLU     5      -2.256  27.265  75.500  1.00  0.00              
ATOM      3  C   GLU     5      -2.051  25.823  75.880  1.00  0.00              
ATOM      4  O   GLU     5      -1.771  25.479  77.030  1.00  0.00              
ATOM      5  N   GLY     6      -2.296  24.969  74.911  1.00  0.00              
ATOM      6  CA  GLY     6      -2.191  23.573  75.212  1.00  0.00              
ATOM      7  C   GLY     6      -0.758  23.124  75.363  1.00  0.00              
ATOM      8  O   GLY     6      -0.480  22.063  75.899  1.00  0.00              
ATOM      9  N   VAL     7       0.186  23.957  74.983  1.00  0.00              
ATOM     10  CA  VAL     7       1.565  23.566  75.232  1.00  0.00              
ATOM     11  C   VAL     7       1.832  24.106  76.663  1.00  0.00              
ATOM     12  O   VAL     7       2.600  23.549  77.436  1.00  0.00              
ATOM     13  N   LEU     8       1.078  25.108  77.077  1.00  0.00              
ATOM     14  CA  LEU     8       1.205  25.517  78.432  1.00  0.00              
ATOM     15  C   LEU     8       0.611  24.509  79.379  1.00  0.00              
ATOM     16  O   LEU     8       1.058  24.384  80.516  1.00  0.00              
ATOM     17  N   LYS     9      -0.347  23.728  78.899  1.00  0.00              
ATOM     18  CA  LYS     9      -0.919  22.726  79.773  1.00  0.00              
ATOM     19  C   LYS     9       0.061  21.572  79.913  1.00  0.00              
ATOM     20  O   LYS     9       0.322  21.140  81.029  1.00  0.00              
ATOM     21  N   LYS    10       0.683  21.132  78.822  1.00  0.00              
ATOM     22  CA  LYS    10       1.661  20.048  78.938  1.00  0.00              
ATOM     23  C   LYS    10       2.797  20.382  79.911  1.00  0.00              
ATOM     24  O   LYS    10       3.322  19.497  80.599  1.00  0.00              
ATOM     25  N   LEU    11       3.166  21.656  79.980  1.00  0.00              
ATOM     26  CA  LEU    11       4.208  22.064  80.918  1.00  0.00              
ATOM     27  C   LEU    11       3.599  22.037  82.333  1.00  0.00              
ATOM     28  O   LEU    11       4.103  21.400  83.247  1.00  0.00              
ATOM     29  N   ARG    12       2.478  22.727  82.462  1.00  0.00              
ATOM     30  CA  ARG    12       1.801  22.894  83.717  1.00  0.00              
ATOM     31  C   ARG    12       1.661  21.543  84.339  1.00  0.00              
ATOM     32  O   ARG    12       1.959  21.388  85.509  1.00  0.00              
ATOM     33  N   ALA    13       1.359  20.541  83.518  1.00  0.00              
ATOM     34  CA  ALA    13       1.137  19.198  84.051  1.00  0.00              
ATOM     35  C   ALA    13       2.328  18.646  84.686  1.00  0.00              
ATOM     36  O   ALA    13       2.300  18.186  85.794  1.00  0.00              
ATOM     37  N   VAL    14       3.376  18.548  83.920  1.00  0.00              
ATOM     38  CA  VAL    14       4.510  17.947  84.506  1.00  0.00              
ATOM     39  C   VAL    14       4.987  18.796  85.688  1.00  0.00              
ATOM     40  O   VAL    14       5.305  18.310  86.761  1.00  0.00              
ATOM     41  N   GLU    15       5.038  20.096  85.468  1.00  0.00              
ATOM     42  CA  GLU    15       5.581  20.979  86.448  1.00  0.00              
ATOM     43  C   GLU    15       4.862  20.954  87.752  1.00  0.00              
ATOM     44  O   GLU    15       5.490  21.069  88.799  1.00  0.00              
ATOM     45  N   ASN    16       3.552  20.808  87.720  1.00  0.00              
ATOM     46  CA  ASN    16       2.800  20.774  88.969  1.00  0.00              
ATOM     47  C   ASN    16       3.087  19.544  89.901  1.00  0.00              
ATOM     48  O   ASN    16       3.044  19.644  91.131  1.00  0.00              
ATOM     49  N   GLU    17       3.420  18.404  89.299  1.00  0.00              
ATOM     50  CA  GLU    17       3.787  17.187  90.028  1.00  0.00              
ATOM     51  C   GLU    17       5.070  17.498  90.746  1.00  0.00              
ATOM     52  O   GLU    17       5.273  17.216  91.922  1.00  0.00              
ATOM     53  N   LEU    18       5.945  18.083  89.956  1.00  0.00              
ATOM     54  CA  LEU    18       7.234  18.499  90.399  1.00  0.00              
ATOM     55  C   LEU    18       7.127  19.314  91.705  1.00  0.00              
ATOM     56  O   LEU    18       7.499  18.844  92.769  1.00  0.00              
ATOM     57  N   HIS    19       6.594  20.524  91.625  1.00  0.00              
ATOM     58  CA  HIS    19       6.538  21.400  92.772  1.00  0.00              
ATOM     59  C   HIS    19       5.735  20.804  93.884  1.00  0.00              
ATOM     60  O   HIS    19       5.825  21.246  95.034  1.00  0.00              
ATOM     61  N   TYR    20       4.917  19.819  93.569  1.00  0.00              
ATOM     62  CA  TYR    20       4.188  19.248  94.671  1.00  0.00              
ATOM     63  C   TYR    20       5.181  18.381  95.459  1.00  0.00              
ATOM     64  O   TYR    20       5.347  18.569  96.672  1.00  0.00              
ATOM     65  N   ASN    21       5.886  17.505  94.745  1.00  0.00              
ATOM     66  CA  ASN    21       6.874  16.635  95.362  1.00  0.00              
ATOM     67  C   ASN    21       7.856  17.527  96.115  1.00  0.00              
ATOM     68  O   ASN    21       8.464  17.195  97.114  1.00  0.00              
ATOM     69  N   LYS    22       8.056  18.698  95.585  1.00  0.00              
ATOM     70  CA  LYS    22       9.058  19.467  96.198  1.00  0.00              
ATOM     71  C   LYS    22       8.687  19.958  97.534  1.00  0.00              
ATOM     72  O   LYS    22       9.519  19.981  98.428  1.00  0.00              
ATOM     73  N   SER    23       7.449  20.414  97.641  1.00  0.00              
ATOM     74  CA  SER    23       6.949  20.918  98.892  1.00  0.00              
ATOM     75  C   SER    23       7.007  19.792  99.901  1.00  0.00              
ATOM     76  O   SER    23       7.493  19.964 100.995  1.00  0.00              
ATOM     77  N   LEU    24       6.520  18.624  99.486  1.00  0.00              
ATOM     78  CA  LEU    24       6.516  17.453 100.333  1.00  0.00              
ATOM     79  C   LEU    24       7.933  17.268 100.917  1.00  0.00              
ATOM     80  O   LEU    24       8.140  17.347 102.131  1.00  0.00              
ATOM     81  N   LEU    25       8.915  17.177 100.021  1.00  0.00              
ATOM     82  CA  LEU    25      10.323  17.015 100.375  1.00  0.00              
ATOM     83  C   LEU    25      10.764  18.013 101.436  1.00  0.00              
ATOM     84  O   LEU    25      11.297  17.565 102.452  1.00  0.00              
ATOM     85  N   GLU    26      10.575  19.320 101.195  1.00  0.00              
ATOM     86  CA  GLU    26      10.942  20.355 102.167  1.00  0.00              
ATOM     87  C   GLU    26      10.302  19.873 103.462  1.00  0.00              
ATOM     88  O   GLU    26      10.929  19.822 104.509  1.00  0.00              
ATOM     89  N   GLU    27       9.049  19.458 103.355  1.00  0.00              
ATOM     90  CA  GLU    27       8.308  19.027 104.512  1.00  0.00              
ATOM     91  C   GLU    27       8.966  17.920 105.325  1.00  0.00              
ATOM     92  O   GLU    27       9.041  18.041 106.555  1.00  0.00              
ATOM     93  N   VAL    28       9.496  16.912 104.610  1.00  0.00              
ATOM     94  CA  VAL    28      10.152  15.746 105.193  1.00  0.00              
ATOM     95  C   VAL    28      11.489  16.140 105.719  1.00  0.00              
ATOM     96  O   VAL    28      11.881  15.745 106.795  1.00  0.00              
ATOM     97  N   LYS    29      12.201  16.890 104.909  1.00  0.00              
ATOM     98  CA  LYS    29      13.522  17.312 105.289  1.00  0.00              
ATOM     99  C   LYS    29      13.487  18.080 106.622  1.00  0.00              
ATOM    100  O   LYS    29      14.290  17.814 107.517  1.00  0.00              
ATOM    101  N   ASP    30      12.542  18.999 106.759  1.00  0.00              
ATOM    102  CA  ASP    30      12.395  19.798 107.963  1.00  0.00              
ATOM    103  C   ASP    30      12.475  18.909 109.228  1.00  0.00              
ATOM    104  O   ASP    30      13.278  19.124 110.137  1.00  0.00              
ATOM    105  N   GLU    31      11.685  17.852 109.255  1.00  0.00              
ATOM    106  CA  GLU    31      11.688  17.010 110.424  1.00  0.00              
ATOM    107  C   GLU    31      12.769  15.962 110.393  1.00  0.00              
ATOM    108  O   GLU    31      13.604  15.902 111.274  1.00  0.00              
ATOM    109  N   LEU    32      12.746  15.110 109.390  1.00  0.00              
ATOM    110  CA  LEU    32      13.725  14.049 109.366  1.00  0.00              
ATOM    111  C   LEU    32      14.971  14.147 108.553  1.00  0.00              
ATOM    112  O   LEU    32      15.432  13.120 108.035  1.00  0.00              
END
