REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0063AL009_3 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0063  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0063, translation initiation factor 5A  
REMARK  
METHOD This prediction is based, in part, on a threading algorithm described in  
METHOD three publications:  
METHOD (i) "A polynomial-time algorithm for a class of protein threading  
METHOD problems", by Ying Xu and Edward C. Uberbacher, CABIOS (journal)  
METHOD Vol.12, No.6, 1996 pp.511-517.  
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) "An Efficient Computational Method for Globally Optimal Threading",  
METHOD by Y. Xu, D. Xu, and E.C. Uberbacher, invited paper to appear in  
METHOD Journal of Computational Biology, 1998.  
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 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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1gpr 
ATOM      1  N   LEU     3       6.996  15.455  17.153  1.00  0.00              
ATOM      2  CA  LEU     3       7.707  16.365  18.084  1.00  0.00              
ATOM      3  C   LEU     3       9.177  16.464  17.542  1.00  0.00              
ATOM      4  O   LEU     3       9.709  15.471  17.042  1.00  0.00              
ATOM      5  N   LYS     4       9.815  17.633  17.558  1.00  0.00              
ATOM      6  CA  LYS     4      11.182  17.758  17.027  1.00  0.00              
ATOM      7  C   LYS     4      12.141  16.903  17.883  1.00  0.00              
ATOM      8  O   LYS     4      12.102  16.960  19.108  1.00  0.00              
ATOM      9  N   TRP     5      12.962  16.066  17.261  1.00  0.00              
ATOM     10  CA  TRP     5      14.016  15.319  17.909  1.00  0.00              
ATOM     11  C   TRP     5      15.257  15.375  17.031  1.00  0.00              
ATOM     12  O   TRP     5      15.282  14.805  15.961  1.00  0.00              
ATOM     13  N   VAL     6      16.254  16.132  17.493  1.00  0.00              
ATOM     14  CA  VAL     6      17.523  16.386  16.754  1.00  0.00              
ATOM     15  C   VAL     6      18.691  15.559  17.278  1.00  0.00              
ATOM     16  O   VAL     6      18.709  15.203  18.441  1.00  0.00              
ATOM     17  N   TYR    11      28.362   8.345  14.265  1.00  0.00              
ATOM     18  CA  TYR    11      27.660   7.320  13.446  1.00  0.00              
ATOM     19  C   TYR    11      26.470   6.730  14.199  1.00  0.00              
ATOM     20  O   TYR    11      26.633   6.263  15.274  1.00  0.00              
ATOM     21  N   VAL    12      25.291   6.665  13.632  1.00  0.00              
ATOM     22  CA  VAL    12      24.041   6.178  14.269  1.00  0.00              
ATOM     23  C   VAL    12      23.879   4.740  14.104  1.00  0.00              
ATOM     24  O   VAL    12      24.156   4.208  13.040  1.00  0.00              
ATOM     25  N   GLU    13      23.514   4.082  15.207  1.00  0.00              
ATOM     26  CA  GLU    13      23.374   2.653  15.268  1.00  0.00              
ATOM     27  C   GLU    13      22.093   2.252  15.960  1.00  0.00              
ATOM     28  O   GLU    13      21.605   2.998  16.798  1.00  0.00              
ATOM     29  N   ALA    14      21.578   1.118  15.632  1.00  0.00              
ATOM     30  CA  ALA    14      20.459   0.589  16.330  1.00  0.00              
ATOM     31  C   ALA    14      20.927   0.298  17.740  1.00  0.00              
ATOM     32  O   ALA    14      22.127   0.116  17.934  1.00  0.00              
ATOM     33  N   GLY    20      13.658   1.329  25.074  1.00  0.00              
ATOM     34  CA  GLY    20      14.073   1.200  23.681  1.00  0.00              
ATOM     35  C   GLY    20      14.877   2.430  23.314  1.00  0.00              
ATOM     36  O   GLY    20      14.792   3.402  24.053  1.00  0.00              
ATOM     37  N   SER    21      15.635   2.447  22.199  1.00  0.00              
ATOM     38  CA  SER    21      16.363   3.679  21.886  1.00  0.00              
ATOM     39  C   SER    21      17.276   3.458  20.716  1.00  0.00              
ATOM     40  O   SER    21      16.940   2.660  19.829  1.00  0.00              
ATOM     41  N   TYR    22      18.336   4.242  20.682  1.00  0.00              
ATOM     42  CA  TYR    22      19.265   4.010  19.596  1.00  0.00              
ATOM     43  C   TYR    22      20.659   4.392  20.147  1.00  0.00              
ATOM     44  O   TYR    22      20.779   4.772  21.313  1.00  0.00              
ATOM     45  N   VAL    23      21.711   4.346  19.371  1.00  0.00              
ATOM     46  CA  VAL    23      23.014   4.725  19.938  1.00  0.00              
ATOM     47  C   VAL    23      23.774   5.500  18.879  1.00  0.00              
ATOM     48  O   VAL    23      23.577   5.292  17.676  1.00  0.00              
ATOM     49  N   VAL    24      24.696   6.325  19.346  1.00  0.00              
ATOM     50  CA  VAL    24      25.583   7.021  18.448  1.00  0.00              
ATOM     51  C   VAL    24      27.031   6.759  18.907  1.00  0.00              
ATOM     52  O   VAL    24      27.339   6.802  20.095  1.00  0.00              
ATOM     53  N   ILE    25      27.912   6.437  17.959  1.00  0.00              
ATOM     54  CA  ILE    25      29.370   6.298  18.211  1.00  0.00              
ATOM     55  C   ILE    25      29.932   7.670  17.930  1.00  0.00              
ATOM     56  O   ILE    25      29.974   8.182  16.806  1.00  0.00              
ATOM     57  N   ASP    26      30.274   8.414  18.947  1.00  0.00              
ATOM     58  CA  ASP    26      30.651   9.760  18.677  1.00  0.00              
ATOM     59  C   ASP    26      31.978   9.990  17.972  1.00  0.00              
ATOM     60  O   ASP    26      32.954   9.358  18.292  1.00  0.00              
ATOM     61  N   ARG    31      30.975  16.709  21.895  1.00  0.00              
ATOM     62  CA  ARG    31      30.021  17.632  22.403  1.00  0.00              
ATOM     63  C   ARG    31      28.618  17.000  22.394  1.00  0.00              
ATOM     64  O   ARG    31      28.217  16.283  21.456  1.00  0.00              
ATOM     65  N   VAL    32      27.841  17.235  23.473  1.00  0.00              
ATOM     66  CA  VAL    32      26.498  16.635  23.531  1.00  0.00              
ATOM     67  C   VAL    32      25.517  17.791  23.597  1.00  0.00              
ATOM     68  O   VAL    32      25.702  18.644  24.435  1.00  0.00              
ATOM     69  N   VAL    33      24.520  17.875  22.701  1.00  0.00              
ATOM     70  CA  VAL    33      23.599  18.980  22.762  1.00  0.00              
ATOM     71  C   VAL    33      22.191  18.442  23.013  1.00  0.00              
ATOM     72  O   VAL    33      21.944  17.244  22.864  1.00  0.00              
ATOM     73  N   ALA    48      12.831  20.986  26.210  1.00  0.00              
ATOM     74  CA  ALA    48      12.306  20.194  27.327  1.00  0.00              
ATOM     75  C   ALA    48      13.011  20.606  28.602  1.00  0.00              
ATOM     76  O   ALA    48      13.337  21.767  28.777  1.00  0.00              
ATOM     77  N   ARG    49      13.179  19.690  29.553  1.00  0.00              
ATOM     78  CA  ARG    49      13.724  20.028  30.885  1.00  0.00              
ATOM     79  C   ARG    49      14.739  18.988  31.358  1.00  0.00              
ATOM     80  O   ARG    49      14.600  17.792  31.094  1.00  0.00              
ATOM     81  N   ILE    50      15.722  19.440  32.094  1.00  0.00              
ATOM     82  CA  ILE    50      16.725  18.539  32.551  1.00  0.00              
ATOM     83  C   ILE    50      16.236  17.897  33.803  1.00  0.00              
ATOM     84  O   ILE    50      15.974  18.595  34.742  1.00  0.00              
ATOM     85  N   VAL    51      16.229  16.604  33.874  1.00  0.00              
ATOM     86  CA  VAL    51      15.762  16.012  35.119  1.00  0.00              
ATOM     87  C   VAL    51      16.831  15.589  36.049  1.00  0.00              
ATOM     88  O   VAL    51      16.583  15.500  37.220  1.00  0.00              
ATOM     89  N   ALA    52      17.982  15.189  35.522  1.00  0.00              
ATOM     90  CA  ALA    52      18.990  14.588  36.356  1.00  0.00              
ATOM     91  C   ALA    52      20.341  14.677  35.642  1.00  0.00              
ATOM     92  O   ALA    52      20.486  14.395  34.472  1.00  0.00              
ATOM     93  N   VAL    53      21.340  15.115  36.339  1.00  0.00              
ATOM     94  CA  VAL    53      22.683  15.182  35.822  1.00  0.00              
ATOM     95  C   VAL    53      23.442  14.207  36.746  1.00  0.00              
ATOM     96  O   VAL    53      23.507  14.412  37.978  1.00  0.00              
ATOM     97  N   THR    62      26.173  11.165  32.115  1.00  0.00              
ATOM     98  CA  THR    62      24.872  10.813  31.636  1.00  0.00              
ATOM     99  C   THR    62      23.935  11.885  32.102  1.00  0.00              
ATOM    100  O   THR    62      24.129  12.516  33.143  1.00  0.00              
ATOM    101  N   LEU    63      22.920  12.166  31.326  1.00  0.00              
ATOM    102  CA  LEU    63      21.936  13.245  31.609  1.00  0.00              
ATOM    103  C   LEU    63      20.548  12.696  31.335  1.00  0.00              
ATOM    104  O   LEU    63      20.361  11.914  30.417  1.00  0.00              
ATOM    105  N   SER    64      19.537  13.081  32.137  1.00  0.00              
ATOM    106  CA  SER    64      18.191  12.605  31.905  1.00  0.00              
ATOM    107  C   SER    64      17.375  13.833  31.519  1.00  0.00              
ATOM    108  O   SER    64      17.453  14.922  32.138  1.00  0.00              
ATOM    109  N   LEU    65      16.552  13.689  30.473  1.00  0.00              
ATOM    110  CA  LEU    65      15.762  14.871  30.130  1.00  0.00              
ATOM    111  C   LEU    65      14.344  14.461  29.876  1.00  0.00              
ATOM    112  O   LEU    65      14.078  13.271  29.677  1.00  0.00              
ATOM    113  N   PRO    66      13.463  15.465  29.875  1.00  0.00              
ATOM    114  CA  PRO    66      12.074  15.205  29.520  1.00  0.00              
ATOM    115  C   PRO    66      11.664  16.308  28.531  1.00  0.00              
ATOM    116  O   PRO    66      11.911  17.497  28.769  1.00  0.00              
ATOM    117  N   VAL    67      11.171  15.878  27.378  1.00  0.00              
ATOM    118  CA  VAL    67      10.721  16.773  26.328  1.00  0.00              
ATOM    119  C   VAL    67       9.408  17.413  26.692  1.00  0.00              
ATOM    120  O   VAL    67       8.673  16.768  27.413  1.00  0.00              
ATOM    121  N   GLN    70      10.615  10.747  28.341  1.00  0.00              
ATOM    122  CA  GLN    70      11.807  10.822  29.119  1.00  0.00              
ATOM    123  C   GLN    70      12.931  10.135  28.373  1.00  0.00              
ATOM    124  O   GLN    70      12.741   9.044  27.851  1.00  0.00              
ATOM    125  N   VAL    71      14.103  10.795  28.368  1.00  0.00              
ATOM    126  CA  VAL    71      15.239  10.325  27.611  1.00  0.00              
ATOM    127  C   VAL    71      16.452  10.274  28.489  1.00  0.00              
ATOM    128  O   VAL    71      16.664  11.124  29.340  1.00  0.00              
ATOM    129  N   GLU    72      17.257   9.257  28.321  1.00  0.00              
ATOM    130  CA  GLU    72      18.502   9.254  29.115  1.00  0.00              
ATOM    131  C   GLU    72      19.638   9.209  28.110  1.00  0.00              
ATOM    132  O   GLU    72      19.547   8.399  27.193  1.00  0.00              
ATOM    133  N   VAL    73      20.640  10.026  28.205  1.00  0.00              
ATOM    134  CA  VAL    73      21.735   9.957  27.284  1.00  0.00              
ATOM    135  C   VAL    73      22.919   9.526  28.151  1.00  0.00              
ATOM    136  O   VAL    73      23.224  10.168  29.138  1.00  0.00              
ATOM    137  N   PRO    74      23.511   8.399  27.888  1.00  0.00              
ATOM    138  CA  PRO    74      24.590   7.932  28.780  1.00  0.00              
ATOM    139  C   PRO    74      25.796   7.840  27.938  1.00  0.00              
ATOM    140  O   PRO    74      25.927   6.977  27.074  1.00  0.00              
ATOM    141  N   PHE    79      34.875  14.918  31.765  1.00  0.00              
ATOM    142  CA  PHE    79      33.488  15.374  31.517  1.00  0.00              
ATOM    143  C   PHE    79      33.184  16.702  32.070  1.00  0.00              
ATOM    144  O   PHE    79      33.483  16.919  33.250  1.00  0.00              
ATOM    145  N   THR    80      32.589  17.585  31.236  1.00  0.00              
ATOM    146  CA  THR    80      32.199  18.886  31.741  1.00  0.00              
ATOM    147  C   THR    80      30.701  19.022  31.549  1.00  0.00              
ATOM    148  O   THR    80      30.221  18.622  30.547  1.00  0.00              
ATOM    149  N   ALA    81      29.975  19.582  32.493  1.00  0.00              
ATOM    150  CA  ALA    81      28.538  19.799  32.430  1.00  0.00              
ATOM    151  C   ALA    81      28.179  21.292  32.197  1.00  0.00              
ATOM    152  O   ALA    81      28.822  22.203  32.634  1.00  0.00              
ATOM    153  N   ASP    89      23.982  23.153  24.269  1.00  0.00              
ATOM    154  CA  ASP    89      25.035  22.281  24.773  1.00  0.00              
ATOM    155  C   ASP    89      24.736  21.737  26.150  1.00  0.00              
ATOM    156  O   ASP    89      24.380  22.494  27.087  1.00  0.00              
ATOM    157  N   VAL    90      24.886  20.436  26.301  1.00  0.00              
ATOM    158  CA  VAL    90      24.659  19.878  27.618  1.00  0.00              
ATOM    159  C   VAL    90      25.975  19.477  28.262  1.00  0.00              
ATOM    160  O   VAL    90      26.201  19.685  29.445  1.00  0.00              
ATOM    161  N   ILE    91      26.823  18.826  27.489  1.00  0.00              
ATOM    162  CA  ILE    91      28.084  18.326  28.039  1.00  0.00              
ATOM    163  C   ILE    91      29.247  18.387  27.064  1.00  0.00              
ATOM    164  O   ILE    91      29.107  18.358  25.849  1.00  0.00              
ATOM    165  N   GLN    92      30.427  18.330  27.593  1.00  0.00              
ATOM    166  CA  GLN    92      31.541  18.272  26.701  1.00  0.00              
ATOM    167  C   GLN    92      32.483  17.232  27.263  1.00  0.00              
ATOM    168  O   GLN    92      32.612  17.151  28.490  1.00  0.00              
ATOM    169  N   LEU    93      32.956  16.314  26.371  1.00  0.00              
ATOM    170  CA  LEU    93      33.785  15.172  26.726  1.00  0.00              
ATOM    171  C   LEU    93      35.100  15.278  26.024  1.00  0.00              
ATOM    172  O   LEU    93      35.112  15.535  24.798  1.00  0.00              
ATOM    173  N   MET    96      37.518  13.394  24.475  1.00  0.00              
ATOM    174  CA  MET    96      37.615  12.045  23.985  1.00  0.00              
ATOM    175  C   MET    96      38.910  11.364  24.158  1.00  0.00              
ATOM    176  O   MET    96      38.935  10.176  24.275  1.00  0.00              
ATOM    177  N   ARG    97      40.003  12.080  24.055  1.00  0.00              
ATOM    178  CA  ARG    97      41.329  11.488  24.169  1.00  0.00              
ATOM    179  C   ARG    97      41.634  11.018  25.577  1.00  0.00              
ATOM    180  O   ARG    97      42.386  10.071  25.755  1.00  0.00              
ATOM    181  N   ASP    98      40.999  11.661  26.559  1.00  0.00              
ATOM    182  CA  ASP    98      41.168  11.279  27.961  1.00  0.00              
ATOM    183  C   ASP    98      40.264  10.095  28.288  1.00  0.00              
ATOM    184  O   ASP    98      40.516   9.315  29.176  1.00  0.00              
ATOM    185  N   TYR    99      39.149  10.000  27.568  1.00  0.00              
ATOM    186  CA  TYR    99      38.147   8.987  27.821  1.00  0.00              
ATOM    187  C   TYR    99      38.375   7.726  27.063  1.00  0.00              
ATOM    188  O   TYR    99      38.306   6.687  27.652  1.00  0.00              
ATOM    189  N   LYS   100      38.654   7.860  25.766  1.00  0.00              
ATOM    190  CA  LYS   100      38.828   6.751  24.840  1.00  0.00              
ATOM    191  C   LYS   100      39.719   5.672  25.364  1.00  0.00              
ATOM    192  O   LYS   100      39.369   4.514  25.375  1.00  0.00              
ATOM    193  N   THR   101      40.884   6.011  25.867  1.00  0.00              
ATOM    194  CA  THR   101      41.715   4.917  26.284  1.00  0.00              
ATOM    195  C   THR   101      41.186   4.082  27.433  1.00  0.00              
ATOM    196  O   THR   101      41.502   2.904  27.532  1.00  0.00              
ATOM    197  N   ILE   102      40.329   4.661  28.283  1.00  0.00              
ATOM    198  CA  ILE   102      39.831   4.009  29.448  1.00  0.00              
ATOM    199  C   ILE   102      38.475   3.302  29.446  1.00  0.00              
ATOM    200  O   ILE   102      38.082   2.802  30.475  1.00  0.00              
ATOM    201  N   VAL   104      27.390   5.528  22.650  1.00  0.00              
ATOM    202  CA  VAL   104      26.570   6.224  23.523  1.00  0.00              
ATOM    203  C   VAL   104      25.074   5.916  23.294  1.00  0.00              
ATOM    204  O   VAL   104      24.535   6.378  22.301  1.00  0.00              
ATOM    205  N   PRO   105      24.409   5.219  24.224  1.00  0.00              
ATOM    206  CA  PRO   105      22.987   5.013  24.064  1.00  0.00              
ATOM    207  C   PRO   105      22.190   6.276  24.431  1.00  0.00              
ATOM    208  O   PRO   105      22.524   7.037  25.361  1.00  0.00              
ATOM    209  N   MET   106      21.106   6.440  23.687  1.00  0.00              
ATOM    210  CA  MET   106      20.010   7.359  23.804  1.00  0.00              
ATOM    211  C   MET   106      18.749   6.499  24.020  1.00  0.00              
ATOM    212  O   MET   106      18.335   5.781  23.169  1.00  0.00              
ATOM    213  N   LYS   107      18.250   6.450  25.275  1.00  0.00              
ATOM    214  CA  LYS   107      17.201   5.558  25.698  1.00  0.00              
ATOM    215  C   LYS   107      15.950   6.355  26.070  1.00  0.00              
ATOM    216  O   LYS   107      16.050   7.350  26.809  1.00  0.00              
ATOM    217  N   TYR   108      14.847   5.893  25.539  1.00  0.00              
ATOM    218  CA  TYR   108      13.545   6.457  25.829  1.00  0.00              
ATOM    219  C   TYR   108      13.007   5.611  26.972  1.00  0.00              
ATOM    220  O   TYR   108      12.736   4.438  26.792  1.00  0.00              
ATOM    221  N   VAL   123      11.242   2.248  18.762  1.00  0.00              
ATOM    222  CA  VAL   123      12.093   3.270  18.203  1.00  0.00              
ATOM    223  C   VAL   123      12.625   2.793  16.843  1.00  0.00              
ATOM    224  O   VAL   123      13.081   1.682  16.656  1.00  0.00              
ATOM    225  N   GLU   124      12.622   3.639  15.853  1.00  0.00              
ATOM    226  CA  GLU   124      13.196   3.190  14.586  1.00  0.00              
ATOM    227  C   GLU   124      14.234   4.197  14.070  1.00  0.00              
ATOM    228  O   GLU   124      13.975   5.391  14.107  1.00  0.00              
ATOM    229  N   VAL   125      15.380   3.784  13.569  1.00  0.00              
ATOM    230  CA  VAL   125      16.345   4.799  13.125  1.00  0.00              
ATOM    231  C   VAL   125      16.014   5.233  11.670  1.00  0.00              
ATOM    232  O   VAL   125      15.780   4.396  10.824  1.00  0.00              
ATOM    233  N   ILE   135      15.207   9.662  13.849  1.00  0.00              
ATOM    234  CA  ILE   135      14.594   8.423  14.318  1.00  0.00              
ATOM    235  C   ILE   135      13.096   8.616  14.355  1.00  0.00              
ATOM    236  O   ILE   135      12.593   9.747  14.310  1.00  0.00              
ATOM    237  N   ARG   136      12.399   7.526  14.564  1.00  0.00              
ATOM    238  CA  ARG   136      10.939   7.592  14.625  1.00  0.00              
ATOM    239  C   ARG   136      10.413   6.730  15.721  1.00  0.00              
ATOM    240  O   ARG   136      10.893   5.598  15.832  1.00  0.00              
ATOM    241  N   VAL   137       9.388   7.183  16.454  1.00  0.00              
ATOM    242  CA  VAL   137       8.768   6.343  17.478  1.00  0.00              
ATOM    243  C   VAL   137       7.437   5.925  16.897  1.00  0.00              
ATOM    244  O   VAL   137       6.586   6.763  16.741  1.00  0.00              
END
