REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL009_1_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  
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  
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: 1cos_C 
ATOM      1  N   LEU    22      16.117  -7.364  -2.546  1.00  0.00              
ATOM      2  CA  LEU    22      14.851  -7.320  -1.815  1.00  0.00              
ATOM      3  C   LEU    22      13.946  -8.489  -2.173  1.00  0.00              
ATOM      4  O   LEU    22      13.277  -9.110  -1.301  1.00  0.00              
ATOM      5  N   ALA    23      13.913  -8.796  -3.490  1.00  0.00              
ATOM      6  CA  ALA    23      13.069  -9.897  -3.944  1.00  0.00              
ATOM      7  C   ALA    23      13.481 -11.200  -3.343  1.00  0.00              
ATOM      8  O   ALA    23      12.651 -12.075  -3.079  1.00  0.00              
ATOM      9  N   ALA    24      14.778 -11.382  -3.223  1.00  0.00              
ATOM     10  CA  ALA    24      15.169 -12.611  -2.598  1.00  0.00              
ATOM     11  C   ALA    24      14.694 -12.647  -1.140  1.00  0.00              
ATOM     12  O   ALA    24      14.143 -13.626  -0.709  1.00  0.00              
ATOM     13  N   LEU    25      14.762 -11.522  -0.456  1.00  0.00              
ATOM     14  CA  LEU    25      14.375 -11.388   0.914  1.00  0.00              
ATOM     15  C   LEU    25      12.850 -11.532   1.066  1.00  0.00              
ATOM     16  O   LEU    25      12.408 -12.292   1.930  1.00  0.00              
ATOM     17  N   GLU    26      12.032 -10.866   0.218  1.00  0.00              
ATOM     18  CA  GLU    26      10.566 -11.065   0.303  1.00  0.00              
ATOM     19  C   GLU    26      10.237 -12.544   0.047  1.00  0.00              
ATOM     20  O   GLU    26       9.309 -13.113   0.563  1.00  0.00              
ATOM     21  N   SER    27      10.996 -13.167  -0.852  1.00  0.00              
ATOM     22  CA  SER    27      10.804 -14.574  -1.184  1.00  0.00              
ATOM     23  C   SER    27      10.771 -15.448   0.068  1.00  0.00              
ATOM     24  O   SER    27       9.789 -16.080   0.346  1.00  0.00              
ATOM     25  N   GLU    28      11.763 -15.248   0.907  1.00  0.00              
ATOM     26  CA  GLU    28      12.029 -15.969   2.126  1.00  0.00              
ATOM     27  C   GLU    28      10.956 -15.768   3.202  1.00  0.00              
ATOM     28  O   GLU    28      10.440 -16.723   3.832  1.00  0.00              
ATOM     29  N   LEU    29      10.611 -14.509   3.401  1.00  0.00              
ATOM     30  CA  LEU    29       9.533 -14.152   4.280  1.00  0.00              
ATOM     31  C   LEU    29       8.308 -14.909   3.867  1.00  0.00              
ATOM     32  O   LEU    29       7.687 -15.505   4.752  1.00  0.00              
ATOM     33  N   GLN    30       7.956 -14.900   2.526  1.00  0.00              
ATOM     34  CA  GLN    30       6.742 -15.564   2.023  1.00  0.00              
ATOM     35  C   GLN    30       6.769 -17.071   2.162  1.00  0.00              
ATOM     36  O   GLN    30       5.751 -17.731   2.412  1.00  0.00              
ATOM     37  N   ALA    31       7.920 -17.670   1.984  1.00  0.00              
ATOM     38  CA  ALA    31       8.019 -19.110   2.217  1.00  0.00              
ATOM     39  C   ALA    31       7.917 -19.524   3.708  1.00  0.00              
ATOM     40  O   ALA    31       7.285 -20.528   4.021  1.00  0.00              
ATOM     41  N   LEU    32       8.467 -18.699   4.643  1.00  0.00              
ATOM     42  CA  LEU    32       8.312 -18.941   6.080  1.00  0.00              
ATOM     43  C   LEU    32       6.875 -18.756   6.494  1.00  0.00              
ATOM     44  O   LEU    32       6.285 -19.515   7.281  1.00  0.00              
ATOM     45  N   GLU    33       6.349 -17.646   6.051  1.00  0.00              
ATOM     46  CA  GLU    33       4.964 -17.384   6.315  1.00  0.00              
ATOM     47  C   GLU    33       4.044 -18.540   5.919  1.00  0.00              
ATOM     48  O   GLU    33       3.062 -18.790   6.617  1.00  0.00              
ATOM     49  N   LYS    34       4.432 -19.320   4.906  1.00  0.00              
ATOM     50  CA  LYS    34       3.589 -20.412   4.463  1.00  0.00              
ATOM     51  C   LYS    34       3.668 -21.532   5.420  1.00  0.00              
ATOM     52  O   LYS    34       2.764 -22.350   5.571  1.00  0.00              
ATOM     53  N   LYS    35       4.872 -21.641   5.924  1.00  0.00              
ATOM     54  CA  LYS    35       5.192 -22.689   6.831  1.00  0.00              
ATOM     55  C   LYS    35       4.590 -22.524   8.202  1.00  0.00              
ATOM     56  O   LYS    35       4.054 -23.508   8.710  1.00  0.00              
ATOM     57  N   LEU    36       4.574 -21.268   8.706  1.00  0.00              
ATOM     58  CA  LEU    36       3.894 -20.896   9.965  1.00  0.00              
ATOM     59  C   LEU    36       2.372 -21.088   9.865  1.00  0.00              
ATOM     60  O   LEU    36       1.708 -21.020  10.873  1.00  0.00              
ATOM     61  N   ALA    37       1.838 -21.040   8.630  1.00  0.00              
ATOM     62  CA  ALA    37       0.446 -21.203   8.236  1.00  0.00              
ATOM     63  C   ALA    37       0.102 -22.689   8.336  1.00  0.00              
ATOM     64  O   ALA    37      -0.898 -23.067   8.933  1.00  0.00              
ATOM     65  N   ALA    38       0.990 -23.512   7.774  1.00  0.00              
ATOM     66  CA  ALA    38       0.963 -24.980   7.788  1.00  0.00              
ATOM     67  C   ALA    38       0.785 -25.541   9.190  1.00  0.00              
ATOM     68  O   ALA    38      -0.268 -26.062   9.487  1.00  0.00              
ATOM     69  N   LEU    39       1.817 -25.389  10.037  1.00  0.00              
ATOM     70  CA  LEU    39       1.831 -25.723  11.461  1.00  0.00              
ATOM     71  C   LEU    39       0.609 -25.211  12.227  1.00  0.00              
ATOM     72  O   LEU    39       0.020 -25.949  13.028  1.00  0.00              
ATOM     73  N   LYS    40       0.234 -23.948  11.973  1.00  0.00              
ATOM     74  CA  LYS    40      -0.953 -23.343  12.576  1.00  0.00              
ATOM     75  C   LYS    40      -2.245 -24.007  12.119  1.00  0.00              
ATOM     76  O   LYS    40      -3.206 -24.167  12.863  1.00  0.00              
ATOM     77  N   SER    41      -2.207 -24.517  10.911  1.00  0.00              
ATOM     78  CA  SER    41      -3.332 -25.246  10.432  1.00  0.00              
ATOM     79  C   SER    41      -3.463 -26.533  11.253  1.00  0.00              
ATOM     80  O   SER    41      -4.557 -26.852  11.740  1.00  0.00              
ATOM     81  N   LYS    42      -2.321 -27.202  11.518  1.00  0.00              
ATOM     82  CA  LYS    42      -2.242 -28.411  12.370  1.00  0.00              
ATOM     83  C   LYS    42      -2.624 -28.241  13.847  1.00  0.00              
ATOM     84  O   LYS    42      -3.324 -29.069  14.380  1.00  0.00              
ATOM     85  N   LEU    43      -2.147 -27.213  14.544  1.00  0.00              
ATOM     86  CA  LEU    43      -2.462 -27.119  15.957  1.00  0.00              
ATOM     87  C   LEU    43      -3.945 -27.040  16.206  1.00  0.00              
ATOM     88  O   LEU    43      -4.535 -27.934  16.816  1.00  0.00              
ATOM     89  N   GLN    44      -4.529 -25.924  15.770  1.00  0.00              
ATOM     90  CA  GLN    44      -5.943 -25.671  15.951  1.00  0.00              
ATOM     91  C   GLN    44      -6.849 -26.812  15.407  1.00  0.00              
ATOM     92  O   GLN    44      -8.048 -26.843  15.652  1.00  0.00              
ATOM     93  N   ALA    45      -6.259 -27.808  14.710  1.00  0.00              
ATOM     94  CA  ALA    45      -6.972 -29.032  14.336  1.00  0.00              
ATOM     95  C   ALA    45      -6.894 -30.097  15.471  1.00  0.00              
ATOM     96  O   ALA    45      -7.823 -30.861  15.752  1.00  0.00              
ATOM     97  N   LEU    46      -5.757 -30.136  16.159  1.00  0.00              
ATOM     98  CA  LEU    46      -5.634 -30.975  17.292  1.00  0.00              
ATOM     99  C   LEU    46      -6.554 -30.391  18.368  1.00  0.00              
ATOM    100  O   LEU    46      -7.505 -31.022  18.833  1.00  0.00              
END
