REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL009_4_1 
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 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 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  4 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     2      10.611 -14.509   3.401  1.00  0.00              
ATOM      2  CA  LEU     2       9.533 -14.152   4.280  1.00  0.00              
ATOM      3  C   LEU     2       8.308 -14.909   3.867  1.00  0.00              
ATOM      4  O   LEU     2       7.687 -15.505   4.752  1.00  0.00              
ATOM      5  N   ALA     3       7.956 -14.900   2.526  1.00  0.00              
ATOM      6  CA  ALA     3       6.742 -15.564   2.023  1.00  0.00              
ATOM      7  C   ALA     3       6.769 -17.071   2.162  1.00  0.00              
ATOM      8  O   ALA     3       5.751 -17.731   2.412  1.00  0.00              
ATOM      9  N   ALA     4       7.920 -17.670   1.984  1.00  0.00              
ATOM     10  CA  ALA     4       8.019 -19.110   2.217  1.00  0.00              
ATOM     11  C   ALA     4       7.917 -19.524   3.708  1.00  0.00              
ATOM     12  O   ALA     4       7.285 -20.528   4.021  1.00  0.00              
ATOM     13  N   LEU     5       8.467 -18.699   4.643  1.00  0.00              
ATOM     14  CA  LEU     5       8.312 -18.941   6.080  1.00  0.00              
ATOM     15  C   LEU     5       6.875 -18.756   6.494  1.00  0.00              
ATOM     16  O   LEU     5       6.285 -19.515   7.281  1.00  0.00              
ATOM     17  N   LYS     6       6.349 -17.646   6.051  1.00  0.00              
ATOM     18  CA  LYS     6       4.964 -17.384   6.315  1.00  0.00              
ATOM     19  C   LYS     6       4.044 -18.540   5.919  1.00  0.00              
ATOM     20  O   LYS     6       3.062 -18.790   6.617  1.00  0.00              
ATOM     21  N   SER     7       4.432 -19.320   4.906  1.00  0.00              
ATOM     22  CA  SER     7       3.589 -20.412   4.463  1.00  0.00              
ATOM     23  C   SER     7       3.668 -21.532   5.420  1.00  0.00              
ATOM     24  O   SER     7       2.764 -22.350   5.571  1.00  0.00              
ATOM     25  N   GLU     8       4.872 -21.641   5.924  1.00  0.00              
ATOM     26  CA  GLU     8       5.192 -22.689   6.831  1.00  0.00              
ATOM     27  C   GLU     8       4.590 -22.524   8.202  1.00  0.00              
ATOM     28  O   GLU     8       4.054 -23.508   8.710  1.00  0.00              
ATOM     29  N   LEU     9       4.574 -21.268   8.706  1.00  0.00              
ATOM     30  CA  LEU     9       3.894 -20.896   9.965  1.00  0.00              
ATOM     31  C   LEU     9       2.372 -21.088   9.865  1.00  0.00              
ATOM     32  O   LEU     9       1.708 -21.020  10.873  1.00  0.00              
ATOM     33  N   GLN    10       1.838 -21.040   8.630  1.00  0.00              
ATOM     34  CA  GLN    10       0.446 -21.203   8.236  1.00  0.00              
ATOM     35  C   GLN    10       0.102 -22.689   8.336  1.00  0.00              
ATOM     36  O   GLN    10      -0.898 -23.067   8.933  1.00  0.00              
ATOM     37  N   ALA    11       0.990 -23.512   7.774  1.00  0.00              
ATOM     38  CA  ALA    11       0.963 -24.980   7.788  1.00  0.00              
ATOM     39  C   ALA    11       0.785 -25.541   9.190  1.00  0.00              
ATOM     40  O   ALA    11      -0.268 -26.062   9.487  1.00  0.00              
ATOM     41  N   LEU    12       1.817 -25.389  10.037  1.00  0.00              
ATOM     42  CA  LEU    12       1.831 -25.723  11.461  1.00  0.00              
ATOM     43  C   LEU    12       0.609 -25.211  12.227  1.00  0.00              
ATOM     44  O   LEU    12       0.020 -25.949  13.028  1.00  0.00              
ATOM     45  N   LYS    13       0.234 -23.948  11.973  1.00  0.00              
ATOM     46  CA  LYS    13      -0.953 -23.343  12.576  1.00  0.00              
ATOM     47  C   LYS    13      -2.245 -24.007  12.119  1.00  0.00              
ATOM     48  O   LYS    13      -3.206 -24.167  12.863  1.00  0.00              
ATOM     49  N   LYS    14      -2.207 -24.517  10.911  1.00  0.00              
ATOM     50  CA  LYS    14      -3.332 -25.246  10.432  1.00  0.00              
ATOM     51  C   LYS    14      -3.463 -26.533  11.253  1.00  0.00              
ATOM     52  O   LYS    14      -4.557 -26.852  11.740  1.00  0.00              
ATOM     53  N   GLU    15      -2.321 -27.202  11.518  1.00  0.00              
ATOM     54  CA  GLU    15      -2.242 -28.411  12.370  1.00  0.00              
ATOM     55  C   GLU    15      -2.624 -28.241  13.847  1.00  0.00              
ATOM     56  O   GLU    15      -3.324 -29.069  14.380  1.00  0.00              
END
