REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0059AL009_4 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0059  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0059,  Sm D3 protein (the N-terminal 75 residues)  
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  4   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ay6_H 
ATOM      1  N   HIS    16       8.878   4.462  14.836  1.00  0.00              
ATOM      2  CA  HIS    16       9.047   2.997  14.495  1.00  0.00              
ATOM      3  C   HIS    16       9.732   2.911  13.139  1.00  0.00              
ATOM      4  O   HIS    16       9.314   3.524  12.133  1.00  0.00              
ATOM      5  N   ILE    17      10.769   2.083  13.171  1.00  0.00              
ATOM      6  CA  ILE    17      11.649   1.816  12.084  1.00  0.00              
ATOM      7  C   ILE    17      11.693   0.337  11.754  1.00  0.00              
ATOM      8  O   ILE    17      11.608  -0.542  12.651  1.00  0.00              
ATOM      9  N   VAL    18      11.653   0.005  10.489  1.00  0.00              
ATOM     10  CA  VAL    18      11.787  -1.434  10.084  1.00  0.00              
ATOM     11  C   VAL    18      13.195  -1.616   9.525  1.00  0.00              
ATOM     12  O   VAL    18      13.634  -0.909   8.623  1.00  0.00              
ATOM     13  N   THR    19      13.880  -2.620  10.105  1.00  0.00              
ATOM     14  CA  THR    19      15.231  -3.044   9.611  1.00  0.00              
ATOM     15  C   THR    19      14.941  -4.171   8.533  1.00  0.00              
ATOM     16  O   THR    19      14.360  -5.203   8.848  1.00  0.00              
ATOM     17  N   CYS    20      15.405  -3.810   7.349  1.00  0.00              
ATOM     18  CA  CYS    20      15.075  -4.572   6.121  1.00  0.00              
ATOM     19  C   CYS    20      16.244  -5.056   5.326  1.00  0.00              
ATOM     20  O   CYS    20      17.150  -4.333   4.853  1.00  0.00              
ATOM     21  N   GLU    21      16.258  -6.394   5.179  1.00  0.00              
ATOM     22  CA  GLU    21      17.273  -7.046   4.336  1.00  0.00              
ATOM     23  C   GLU    21      16.970  -6.878   2.820  1.00  0.00              
ATOM     24  O   GLU    21      15.853  -7.136   2.378  1.00  0.00              
ATOM     25  N   GLU    26      13.694  -9.267   3.402  1.00  0.00              
ATOM     26  CA  GLU    26      13.038  -9.795   4.599  1.00  0.00              
ATOM     27  C   GLU    26      13.253  -8.849   5.780  1.00  0.00              
ATOM     28  O   GLU    26      14.209  -8.096   5.802  1.00  0.00              
ATOM     29  N   VAL    27      12.365  -8.908   6.710  1.00  0.00              
ATOM     30  CA  VAL    27      12.414  -8.116   7.922  1.00  0.00              
ATOM     31  C   VAL    27      13.476  -8.813   8.812  1.00  0.00              
ATOM     32  O   VAL    27      13.248  -9.971   9.127  1.00  0.00              
ATOM     33  N   TYR    28      14.419  -7.961   9.224  1.00  0.00              
ATOM     34  CA  TYR    28      15.471  -8.255  10.158  1.00  0.00              
ATOM     35  C   TYR    28      15.083  -8.003  11.626  1.00  0.00              
ATOM     36  O   TYR    28      14.985  -8.895  12.459  1.00  0.00              
ATOM     37  N   ARG    29      14.567  -6.794  11.896  1.00  0.00              
ATOM     38  CA  ARG    29      14.320  -6.335  13.316  1.00  0.00              
ATOM     39  C   ARG    29      13.623  -4.952  13.217  1.00  0.00              
ATOM     40  O   ARG    29      13.564  -4.321  12.145  1.00  0.00              
ATOM     41  N   GLY    30      13.166  -4.493  14.399  1.00  0.00              
ATOM     42  CA  GLY    30      12.620  -3.140  14.598  1.00  0.00              
ATOM     43  C   GLY    30      13.841  -2.251  14.898  1.00  0.00              
ATOM     44  O   GLY    30      15.009  -2.642  15.153  1.00  0.00              
ATOM     45  N   LYS    31      13.517  -0.979  15.051  1.00  0.00              
ATOM     46  CA  LYS    31      14.547   0.059  15.352  1.00  0.00              
ATOM     47  C   LYS    31      13.672   1.343  15.655  1.00  0.00              
ATOM     48  O   LYS    31      12.428   1.128  15.609  1.00  0.00              
ATOM     49  N   LEU    32      14.431   2.369  16.028  1.00  0.00              
ATOM     50  CA  LEU    32      13.704   3.636  16.319  1.00  0.00              
ATOM     51  C   LEU    32      14.465   4.831  15.812  1.00  0.00              
ATOM     52  O   LEU    32      15.696   4.971  15.683  1.00  0.00              
ATOM     53  N   ILE    33      13.651   5.862  15.465  1.00  0.00              
ATOM     54  CA  ILE    33      14.197   7.112  14.887  1.00  0.00              
ATOM     55  C   ILE    33      14.374   8.127  16.062  1.00  0.00              
ATOM     56  O   ILE    33      13.361   8.334  16.798  1.00  0.00              
ATOM     57  N   CYS    41      19.653   9.574  12.606  1.00  0.00              
ATOM     58  CA  CYS    41      20.121   8.469  13.506  1.00  0.00              
ATOM     59  C   CYS    41      18.971   7.592  13.908  1.00  0.00              
ATOM     60  O   CYS    41      17.857   8.004  14.282  1.00  0.00              
ATOM     61  N   GLN    42      19.287   6.292  13.930  1.00  0.00              
ATOM     62  CA  GLN    42      18.393   5.227  14.232  1.00  0.00              
ATOM     63  C   GLN    42      19.000   4.373  15.372  1.00  0.00              
ATOM     64  O   GLN    42      20.215   4.179  15.254  1.00  0.00              
ATOM     65  N   MET    43      18.151   3.980  16.276  1.00  0.00              
ATOM     66  CA  MET    43      18.633   3.150  17.421  1.00  0.00              
ATOM     67  C   MET    43      18.070   1.735  17.301  1.00  0.00              
ATOM     68  O   MET    43      16.887   1.597  17.076  1.00  0.00              
ATOM     69  N   SER    44      18.995   0.798  17.554  1.00  0.00              
ATOM     70  CA  SER    44      18.564  -0.623  17.498  1.00  0.00              
ATOM     71  C   SER    44      19.401  -1.463  18.480  1.00  0.00              
ATOM     72  O   SER    44      20.189  -0.929  19.211  1.00  0.00              
ATOM     73  N   ILE    46      21.780  -3.708   4.215  1.00  0.00              
ATOM     74  CA  ILE    46      20.475  -3.304   4.702  1.00  0.00              
ATOM     75  C   ILE    46      19.897  -1.974   4.243  1.00  0.00              
ATOM     76  O   ILE    46      20.634  -1.029   3.994  1.00  0.00              
ATOM     77  N   THR    47      18.601  -1.995   4.422  1.00  0.00              
ATOM     78  CA  THR    47      17.713  -0.815   4.236  1.00  0.00              
ATOM     79  C   THR    47      16.902  -0.523   5.512  1.00  0.00              
ATOM     80  O   THR    47      16.364  -1.407   6.160  1.00  0.00              
ATOM     81  N   VAL    48      16.673   0.768   5.748  1.00  0.00              
ATOM     82  CA  VAL    48      15.813   1.239   6.868  1.00  0.00              
ATOM     83  C   VAL    48      14.496   1.741   6.256  1.00  0.00              
ATOM     84  O   VAL    48      14.570   2.562   5.376  1.00  0.00              
ATOM     85  N   THR    49      13.361   1.318   6.711  1.00  0.00              
ATOM     86  CA  THR    49      12.056   1.729   6.268  1.00  0.00              
ATOM     87  C   THR    49      11.378   2.458   7.418  1.00  0.00              
ATOM     88  O   THR    49      11.092   1.852   8.486  1.00  0.00              
ATOM     89  N   TYR    50      10.926   3.710   7.178  1.00  0.00              
ATOM     90  CA  TYR    50      10.298   4.599   8.159  1.00  0.00              
ATOM     91  C   TYR    50       8.953   5.113   7.689  1.00  0.00              
ATOM     92  O   TYR    50       8.743   5.374   6.514  1.00  0.00              
ATOM     93  N   ARG    54       9.351   6.054   3.844  1.00  0.00              
ATOM     94  CA  ARG    54      10.566   6.565   3.242  1.00  0.00              
ATOM     95  C   ARG    54      11.648   5.477   3.510  1.00  0.00              
ATOM     96  O   ARG    54      11.731   4.966   4.685  1.00  0.00              
ATOM     97  N   VAL    55      12.373   5.148   2.491  1.00  0.00              
ATOM     98  CA  VAL    55      13.386   4.060   2.608  1.00  0.00              
ATOM     99  C   VAL    55      14.741   4.705   2.686  1.00  0.00              
ATOM    100  O   VAL    55      14.941   5.729   1.986  1.00  0.00              
ATOM    101  N   ALA    56      15.678   4.390   3.536  1.00  0.00              
ATOM    102  CA  ALA    56      16.996   5.056   3.502  1.00  0.00              
ATOM    103  C   ALA    56      18.096   3.972   3.536  1.00  0.00              
ATOM    104  O   ALA    56      17.935   2.856   4.002  1.00  0.00              
ATOM    105  N   GLN    57      19.266   4.468   3.171  1.00  0.00              
ATOM    106  CA  GLN    57      20.493   3.629   3.143  1.00  0.00              
ATOM    107  C   GLN    57      21.302   4.148   4.339  1.00  0.00              
ATOM    108  O   GLN    57      20.994   5.295   4.747  1.00  0.00              
ATOM    109  N   LEU    58      22.166   3.253   4.810  1.00  0.00              
ATOM    110  CA  LEU    58      22.968   3.622   5.986  1.00  0.00              
ATOM    111  C   LEU    58      24.315   4.144   5.544  1.00  0.00              
ATOM    112  O   LEU    58      24.862   3.532   4.600  1.00  0.00              
ATOM    113  N   GLU    59      24.792   5.109   6.270  1.00  0.00              
ATOM    114  CA  GLU    59      26.101   5.685   6.079  1.00  0.00              
ATOM    115  C   GLU    59      27.097   4.861   6.929  1.00  0.00              
ATOM    116  O   GLU    59      28.218   4.439   6.524  1.00  0.00              
ATOM    117  N   GLN    60      26.657   4.521   8.157  1.00  0.00              
ATOM    118  CA  GLN    60      27.649   3.804   9.013  1.00  0.00              
ATOM    119  C   GLN    60      26.921   3.189  10.168  1.00  0.00              
ATOM    120  O   GLN    60      25.944   3.787  10.662  1.00  0.00              
ATOM    121  N   VAL    61      27.432   2.074  10.607  1.00  0.00              
ATOM    122  CA  VAL    61      26.890   1.347  11.783  1.00  0.00              
ATOM    123  C   VAL    61      27.852   1.500  12.953  1.00  0.00              
ATOM    124  O   VAL    61      29.075   1.415  12.730  1.00  0.00              
ATOM    125  N   TYR    62      27.357   1.729  14.141  1.00  0.00              
ATOM    126  CA  TYR    62      28.139   1.833  15.362  1.00  0.00              
ATOM    127  C   TYR    62      27.544   0.889  16.423  1.00  0.00              
ATOM    128  O   TYR    62      26.387   1.034  16.840  1.00  0.00              
ATOM    129  N   ILE    63      28.434  -0.055  16.785  1.00  0.00              
ATOM    130  CA  ILE    63      28.019  -0.993  17.874  1.00  0.00              
ATOM    131  C   ILE    63      28.719  -0.591  19.169  1.00  0.00              
ATOM    132  O   ILE    63      29.882  -0.326  19.067  1.00  0.00              
ATOM    133  N   ARG    69      23.018  -0.369  19.359  1.00  0.00              
ATOM    134  CA  ARG    69      23.769   0.057  18.194  1.00  0.00              
ATOM    135  C   ARG    69      22.981   1.312  17.680  1.00  0.00              
ATOM    136  O   ARG    69      21.740   1.316  17.809  1.00  0.00              
ATOM    137  N   PHE    70      23.799   2.155  17.029  1.00  0.00              
ATOM    138  CA  PHE    70      23.349   3.313  16.258  1.00  0.00              
ATOM    139  C   PHE    70      23.687   3.139  14.774  1.00  0.00              
ATOM    140  O   PHE    70      24.772   2.604  14.371  1.00  0.00              
ATOM    141  N   LEU    71      22.770   3.632  13.940  1.00  0.00              
ATOM    142  CA  LEU    71      22.920   3.592  12.465  1.00  0.00              
ATOM    143  C   LEU    71      22.699   5.018  11.958  1.00  0.00              
ATOM    144  O   LEU    71      21.687   5.642  12.370  1.00  0.00              
ATOM    145  N   ILE    72      23.635   5.560  11.274  1.00  0.00              
ATOM    146  CA  ILE    72      23.468   6.949  10.740  1.00  0.00              
ATOM    147  C   ILE    72      23.095   6.808   9.260  1.00  0.00              
ATOM    148  O   ILE    72      23.705   6.027   8.486  1.00  0.00              
ATOM    149  N   LEU    73      21.968   7.493   8.972  1.00  0.00              
ATOM    150  CA  LEU    73      21.449   7.441   7.586  1.00  0.00              
ATOM    151  C   LEU    73      22.359   8.242   6.663  1.00  0.00              
ATOM    152  O   LEU    73      22.915   9.221   7.072  1.00  0.00              
END
