REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0063AL009_5 
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  5  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1prs 
ATOM      1  N   LEU     3      12.263   4.125 -18.699  1.00  0.00              
ATOM      2  CA  LEU     3      11.641   3.658 -17.436  1.00  0.00              
ATOM      3  C   LEU     3      12.138   4.487 -16.260  1.00  0.00              
ATOM      4  O   LEU     3      13.223   5.036 -16.303  1.00  0.00              
ATOM      5  N   LYS     4      11.326   4.573 -15.236  1.00  0.00              
ATOM      6  CA  LYS     4      11.721   5.360 -14.036  1.00  0.00              
ATOM      7  C   LYS     4      11.505   4.532 -12.781  1.00  0.00              
ATOM      8  O   LYS     4      10.392   4.169 -12.459  1.00  0.00              
ATOM      9  N   TRP     5      12.574   4.247 -12.100  1.00  0.00              
ATOM     10  CA  TRP     5      12.461   3.440 -10.862  1.00  0.00              
ATOM     11  C   TRP     5      12.416   4.320  -9.626  1.00  0.00              
ATOM     12  O   TRP     5      12.603   5.515  -9.705  1.00  0.00              
ATOM     13  N   VAL     6      12.155   3.696  -8.509  1.00  0.00              
ATOM     14  CA  VAL     6      12.086   4.440  -7.227  1.00  0.00              
ATOM     15  C   VAL     6      12.935   3.721  -6.196  1.00  0.00              
ATOM     16  O   VAL     6      12.851   2.509  -6.060  1.00  0.00              
ATOM     17  N   TYR    11      13.821   8.922  -7.520  1.00  0.00              
ATOM     18  CA  TYR    11      13.746   8.022  -8.699  1.00  0.00              
ATOM     19  C   TYR    11      14.891   8.260  -9.675  1.00  0.00              
ATOM     20  O   TYR    11      15.643   9.205  -9.547  1.00  0.00              
ATOM     21  N   VAL    12      14.993   7.382 -10.639  1.00  0.00              
ATOM     22  CA  VAL    12      16.067   7.510 -11.653  1.00  0.00              
ATOM     23  C   VAL    12      15.534   7.111 -13.022  1.00  0.00              
ATOM     24  O   VAL    12      14.873   6.103 -13.160  1.00  0.00              
ATOM     25  N   GLU    13      15.836   7.902 -14.015  1.00  0.00              
ATOM     26  CA  GLU    13      15.347   7.573 -15.381  1.00  0.00              
ATOM     27  C   GLU    13      16.374   6.757 -16.164  1.00  0.00              
ATOM     28  O   GLU    13      17.465   7.222 -16.433  1.00  0.00              
ATOM     29  N   ALA    14      15.994   5.544 -16.514  1.00  0.00              
ATOM     30  CA  ALA    14      16.918   4.662 -17.284  1.00  0.00              
ATOM     31  C   ALA    14      16.361   4.423 -18.707  1.00  0.00              
ATOM     32  O   ALA    14      15.193   4.137 -18.867  1.00  0.00              
ATOM     33  N   GLY    20      16.080  -0.642 -23.831  1.00  0.00              
ATOM     34  CA  GLY    20      17.191  -1.554 -24.234  1.00  0.00              
ATOM     35  C   GLY    20      17.506  -2.558 -23.124  1.00  0.00              
ATOM     36  O   GLY    20      16.932  -2.505 -22.053  1.00  0.00              
ATOM     37  N   SER    21      18.420  -3.454 -23.409  1.00  0.00              
ATOM     38  CA  SER    21      18.799  -4.475 -22.399  1.00  0.00              
ATOM     39  C   SER    21      20.132  -4.145 -21.744  1.00  0.00              
ATOM     40  O   SER    21      21.077  -3.767 -22.407  1.00  0.00              
ATOM     41  N   TYR    22      20.182  -4.290 -20.449  1.00  0.00              
ATOM     42  CA  TYR    22      21.440  -3.994 -19.730  1.00  0.00              
ATOM     43  C   TYR    22      21.457  -4.711 -18.388  1.00  0.00              
ATOM     44  O   TYR    22      20.555  -5.477 -18.085  1.00  0.00              
ATOM     45  N   PRO    29      23.999  -5.211 -14.442  1.00  0.00              
ATOM     46  CA  PRO    29      24.913  -4.647 -13.438  1.00  0.00              
ATOM     47  C   PRO    29      26.053  -3.891 -14.095  1.00  0.00              
ATOM     48  O   PRO    29      26.563  -2.943 -13.543  1.00  0.00              
ATOM     49  N   CYS    30      26.440  -4.325 -15.260  1.00  0.00              
ATOM     50  CA  CYS    30      27.548  -3.635 -15.959  1.00  0.00              
ATOM     51  C   CYS    30      27.182  -2.184 -16.240  1.00  0.00              
ATOM     52  O   CYS    30      27.805  -1.267 -15.728  1.00  0.00              
ATOM     53  N   ARG    31      26.171  -1.988 -17.039  1.00  0.00              
ATOM     54  CA  ARG    31      25.776  -0.603 -17.345  1.00  0.00              
ATOM     55  C   ARG    31      25.457   0.136 -16.061  1.00  0.00              
ATOM     56  O   ARG    31      25.867   1.269 -15.866  1.00  0.00              
ATOM     57  N   VAL    32      24.731  -0.515 -15.196  1.00  0.00              
ATOM     58  CA  VAL    32      24.384   0.142 -13.926  1.00  0.00              
ATOM     59  C   VAL    32      25.652   0.522 -13.183  1.00  0.00              
ATOM     60  O   VAL    32      25.716   1.560 -12.556  1.00  0.00              
ATOM     61  N   VAL    33      26.651  -0.332 -13.261  1.00  0.00              
ATOM     62  CA  VAL    33      27.910  -0.011 -12.559  1.00  0.00              
ATOM     63  C   VAL    33      28.331   1.364 -12.981  1.00  0.00              
ATOM     64  O   VAL    33      28.904   2.116 -12.216  1.00  0.00              
ATOM     65  N   GLU    34      28.034   1.671 -14.213  1.00  0.00              
ATOM     66  CA  GLU    34      28.398   3.000 -14.733  1.00  0.00              
ATOM     67  C   GLU    34      27.592   4.064 -14.006  1.00  0.00              
ATOM     68  O   GLU    34      28.101   5.112 -13.664  1.00  0.00              
ATOM     69  N   ILE    35      26.334   3.770 -13.783  1.00  0.00              
ATOM     70  CA  ILE    35      25.468   4.751 -13.077  1.00  0.00              
ATOM     71  C   ILE    35      25.821   4.816 -11.593  1.00  0.00              
ATOM     72  O   ILE    35      26.533   5.702 -11.163  1.00  0.00              
ATOM     73  N   SER    45      10.140   0.613  -6.502  1.00  0.00              
ATOM     74  CA  SER    45       8.887   0.897  -7.269  1.00  0.00              
ATOM     75  C   SER    45       9.230   1.167  -8.726  1.00  0.00              
ATOM     76  O   SER    45      10.385   1.353  -9.060  1.00  0.00              
ATOM     77  N   ALA    46       8.230   1.182  -9.579  1.00  0.00              
ATOM     78  CA  ALA    46       8.518   1.442 -11.018  1.00  0.00              
ATOM     79  C   ALA    46       7.415   2.258 -11.695  1.00  0.00              
ATOM     80  O   ALA    46       6.274   2.251 -11.282  1.00  0.00              
ATOM     81  N   LYS    47       7.808   2.948 -12.730  1.00  0.00              
ATOM     82  CA  LYS    47       6.850   3.787 -13.492  1.00  0.00              
ATOM     83  C   LYS    47       7.234   3.753 -14.966  1.00  0.00              
ATOM     84  O   LYS    47       8.185   4.396 -15.370  1.00  0.00              
ATOM     85  N   VAL    51       6.065   1.372 -24.732  1.00  0.00              
ATOM     86  CA  VAL    51       7.167   0.430 -24.461  1.00  0.00              
ATOM     87  C   VAL    51       6.786  -0.577 -23.390  1.00  0.00              
ATOM     88  O   VAL    51       6.011  -0.290 -22.502  1.00  0.00              
ATOM     89  N   ALA    52       7.355  -1.741 -23.510  1.00  0.00              
ATOM     90  CA  ALA    52       7.079  -2.825 -22.532  1.00  0.00              
ATOM     91  C   ALA    52       8.393  -3.243 -21.886  1.00  0.00              
ATOM     92  O   ALA    52       9.341  -3.558 -22.579  1.00  0.00              
ATOM     93  N   VAL    53       8.431  -3.248 -20.572  1.00  0.00              
ATOM     94  CA  VAL    53       9.692  -3.642 -19.878  1.00  0.00              
ATOM     95  C   VAL    53       9.633  -5.038 -19.282  1.00  0.00              
ATOM     96  O   VAL    53       8.576  -5.569 -19.007  1.00  0.00              
ATOM     97  N   GLY    54      10.800  -5.596 -19.097  1.00  0.00              
ATOM     98  CA  GLY    54      10.908  -6.951 -18.520  1.00  0.00              
ATOM     99  C   GLY    54      12.022  -6.946 -17.485  1.00  0.00              
ATOM    100  O   GLY    54      13.173  -6.758 -17.821  1.00  0.00              
ATOM    101  N   VAL    55      11.675  -7.165 -16.253  1.00  0.00              
ATOM    102  CA  VAL    55      12.729  -7.164 -15.197  1.00  0.00              
ATOM    103  C   VAL    55      13.339  -8.543 -14.971  1.00  0.00              
ATOM    104  O   VAL    55      12.774  -9.555 -15.339  1.00  0.00              
ATOM    105  N   PHE    56      14.498  -8.539 -14.361  1.00  0.00              
ATOM    106  CA  PHE    56      15.204  -9.814 -14.076  1.00  0.00              
ATOM    107  C   PHE    56      15.856  -9.747 -12.694  1.00  0.00              
ATOM    108  O   PHE    56      16.818  -9.021 -12.487  1.00  0.00              
ATOM    109  N   GLN    70      11.850 -13.528 -13.530  1.00  0.00              
ATOM    110  CA  GLN    70      11.718 -12.242 -14.260  1.00  0.00              
ATOM    111  C   GLN    70      10.322 -11.660 -14.097  1.00  0.00              
ATOM    112  O   GLN    70       9.471 -12.238 -13.450  1.00  0.00              
ATOM    113  N   VAL    71      10.120 -10.521 -14.688  1.00  0.00              
ATOM    114  CA  VAL    71       8.797  -9.864 -14.599  1.00  0.00              
ATOM    115  C   VAL    71       8.491  -9.170 -15.909  1.00  0.00              
ATOM    116  O   VAL    71       9.350  -9.042 -16.750  1.00  0.00              
ATOM    117  N   GLU    72       7.278  -8.738 -16.062  1.00  0.00              
ATOM    118  CA  GLU    72       6.907  -8.047 -17.318  1.00  0.00              
ATOM    119  C   GLU    72       5.902  -6.952 -17.028  1.00  0.00              
ATOM    120  O   GLU    72       4.895  -7.188 -16.391  1.00  0.00              
ATOM    121  N   VAL    73       6.184  -5.771 -17.502  1.00  0.00              
ATOM    122  CA  VAL    73       5.244  -4.661 -17.250  1.00  0.00              
ATOM    123  C   VAL    73       5.255  -3.643 -18.376  1.00  0.00              
ATOM    124  O   VAL    73       6.120  -3.653 -19.226  1.00  0.00              
ATOM    125  N   ILE    83      19.093  -6.808 -13.291  1.00  0.00              
ATOM    126  CA  ILE    83      19.038  -6.979 -14.781  1.00  0.00              
ATOM    127  C   ILE    83      17.667  -6.609 -15.331  1.00  0.00              
ATOM    128  O   ILE    83      16.657  -6.878 -14.708  1.00  0.00              
ATOM    129  N   LEU    84      17.650  -5.998 -16.500  1.00  0.00              
ATOM    130  CA  LEU    84      16.334  -5.605 -17.095  1.00  0.00              
ATOM    131  C   LEU    84      16.373  -5.633 -18.631  1.00  0.00              
ATOM    132  O   LEU    84      17.432  -5.619 -19.231  1.00  0.00              
ATOM    133  N   SER    85      15.202  -5.663 -19.232  1.00  0.00              
ATOM    134  CA  SER    85      15.123  -5.693 -20.723  1.00  0.00              
ATOM    135  C   SER    85      13.893  -4.920 -21.208  1.00  0.00              
ATOM    136  O   SER    85      12.774  -5.300 -20.923  1.00  0.00              
ATOM    137  N   VAL    86      14.130  -3.848 -21.939  1.00  0.00              
ATOM    138  CA  VAL    86      12.992  -3.029 -22.458  1.00  0.00              
ATOM    139  C   VAL    86      12.983  -2.981 -23.982  1.00  0.00              
ATOM    140  O   VAL    86      14.013  -2.828 -24.609  1.00  0.00              
ATOM    141  N   SER    87      11.805  -3.107 -24.545  1.00  0.00              
ATOM    142  CA  SER    87      11.683  -3.072 -26.025  1.00  0.00              
ATOM    143  C   SER    87      10.457  -2.267 -26.441  1.00  0.00              
ATOM    144  O   SER    87       9.359  -2.522 -25.987  1.00  0.00              
ATOM    145  N   GLY    88      10.674  -1.304 -27.296  1.00  0.00              
ATOM    146  CA  GLY    88       9.543  -0.457 -27.769  1.00  0.00              
ATOM    147  C   GLY    88       8.287  -1.289 -28.027  1.00  0.00              
ATOM    148  O   GLY    88       8.365  -2.467 -28.312  1.00  0.00              
ATOM    149  N   ILE    91      -6.325   2.745 -18.490  1.00  0.00              
ATOM    150  CA  ILE    91      -7.311   3.291 -17.529  1.00  0.00              
ATOM    151  C   ILE    91      -6.564   3.910 -16.352  1.00  0.00              
ATOM    152  O   ILE    91      -5.451   3.504 -16.059  1.00  0.00              
ATOM    153  N   GLN    92      -7.184   4.871 -15.684  1.00  0.00              
ATOM    154  CA  GLN    92      -6.497   5.521 -14.525  1.00  0.00              
ATOM    155  C   GLN    92      -7.307   5.444 -13.241  1.00  0.00              
ATOM    156  O   GLN    92      -8.426   5.907 -13.177  1.00  0.00              
ATOM    157  N   LEU    93      -6.707   4.859 -12.241  1.00  0.00              
ATOM    158  CA  LEU    93      -7.386   4.723 -10.932  1.00  0.00              
ATOM    159  C   LEU    93      -6.727   5.661  -9.931  1.00  0.00              
ATOM    160  O   LEU    93      -5.554   5.958 -10.056  1.00  0.00              
ATOM    161  N   ILE   102      -2.625   5.281 -10.167  1.00  0.00              
ATOM    162  CA  ILE   102      -2.090   4.092 -10.859  1.00  0.00              
ATOM    163  C   ILE   102      -2.879   3.833 -12.137  1.00  0.00              
ATOM    164  O   ILE   102      -4.039   4.169 -12.220  1.00  0.00              
ATOM    165  N   GLU   103      -2.239   3.239 -13.112  1.00  0.00              
ATOM    166  CA  GLU   103      -2.953   2.957 -14.388  1.00  0.00              
ATOM    167  C   GLU   103      -2.505   1.630 -14.985  1.00  0.00              
ATOM    168  O   GLU   103      -1.387   1.201 -14.775  1.00  0.00              
ATOM    169  N   VAL   104      -3.399   0.993 -15.719  1.00  0.00              
ATOM    170  CA  VAL   104      -3.040  -0.319 -16.343  1.00  0.00              
ATOM    171  C   VAL   104      -3.590  -0.434 -17.785  1.00  0.00              
ATOM    172  O   VAL   104      -4.662   0.061 -18.078  1.00  0.00              
ATOM    173  N   MET   106      -6.516  -5.519 -20.792  1.00  0.00              
ATOM    174  CA  MET   106      -6.139  -6.945 -20.534  1.00  0.00              
ATOM    175  C   MET   106      -6.861  -7.503 -19.300  1.00  0.00              
ATOM    176  O   MET   106      -7.931  -7.045 -18.941  1.00  0.00              
ATOM    177  N   LYS   107      -6.244  -8.490 -18.678  1.00  0.00              
ATOM    178  CA  LYS   107      -6.855  -9.110 -17.467  1.00  0.00              
ATOM    179  C   LYS   107      -5.849  -9.223 -16.325  1.00  0.00              
ATOM    180  O   LYS   107      -4.666  -9.399 -16.548  1.00  0.00              
ATOM    181  N   TYR   108      -6.348  -9.120 -15.122  1.00  0.00              
ATOM    182  CA  TYR   108      -5.461  -9.217 -13.933  1.00  0.00              
ATOM    183  C   TYR   108      -6.153 -10.030 -12.843  1.00  0.00              
ATOM    184  O   TYR   108      -7.368 -10.116 -12.822  1.00  0.00              
ATOM    185  N   GLU   110      -3.218  -6.364  -7.687  1.00  0.00              
ATOM    186  CA  GLU   110      -2.873  -5.687  -6.427  1.00  0.00              
ATOM    187  C   GLU   110      -1.386  -5.332  -6.380  1.00  0.00              
ATOM    188  O   GLU   110      -1.028  -4.167  -6.352  1.00  0.00              
ATOM    189  N   GLU   111      -0.540  -6.341  -6.402  1.00  0.00              
ATOM    190  CA  GLU   111       0.929  -6.065  -6.356  1.00  0.00              
ATOM    191  C   GLU   111       1.475  -5.560  -7.696  1.00  0.00              
ATOM    192  O   GLU   111       2.644  -5.721  -7.978  1.00  0.00              
ATOM    193  N   GLU   112       0.625  -4.981  -8.505  1.00  0.00              
ATOM    194  CA  GLU   112       1.104  -4.463  -9.827  1.00  0.00              
ATOM    195  C   GLU   112       0.615  -3.060 -10.047  1.00  0.00              
ATOM    196  O   GLU   112       1.025  -2.394 -10.978  1.00  0.00              
ATOM    197  N   ALA   113      -0.250  -2.626  -9.194  1.00  0.00              
ATOM    198  CA  ALA   113      -0.775  -1.260  -9.347  1.00  0.00              
ATOM    199  C   ALA   113      -1.145  -0.678  -7.996  1.00  0.00              
ATOM    200  O   ALA   113      -0.785   0.431  -7.683  1.00  0.00              
ATOM    201  N   GLU   122     -12.813   1.051 -21.317  1.00  0.00              
ATOM    202  CA  GLU   122     -13.731   0.895 -20.161  1.00  0.00              
ATOM    203  C   GLU   122     -13.130  -0.058 -19.143  1.00  0.00              
ATOM    204  O   GLU   122     -12.342  -0.919 -19.491  1.00  0.00              
ATOM    205  N   VAL   123     -13.515   0.112 -17.902  1.00  0.00              
ATOM    206  CA  VAL   123     -12.976  -0.771 -16.831  1.00  0.00              
ATOM    207  C   VAL   123     -14.061  -1.637 -16.204  1.00  0.00              
ATOM    208  O   VAL   123     -15.168  -1.193 -15.995  1.00  0.00              
ATOM    209  N   GLU   124     -13.711  -2.870 -15.931  1.00  0.00              
ATOM    210  CA  GLU   124     -14.687  -3.808 -15.310  1.00  0.00              
ATOM    211  C   GLU   124     -14.042  -4.475 -14.098  1.00  0.00              
ATOM    212  O   GLU   124     -12.971  -5.039 -14.202  1.00  0.00              
ATOM    213  N   VAL   125     -14.712  -4.404 -12.966  1.00  0.00              
ATOM    214  CA  VAL   125     -14.138  -5.033 -11.729  1.00  0.00              
ATOM    215  C   VAL   125     -14.840  -6.330 -11.332  1.00  0.00              
ATOM    216  O   VAL   125     -16.020  -6.506 -11.566  1.00  0.00              
ATOM    217  N   TRP   126     -14.070  -7.217 -10.730  1.00  0.00              
ATOM    218  CA  TRP   126     -14.621  -8.528 -10.284  1.00  0.00              
ATOM    219  C   TRP   126     -14.426  -8.684  -8.782  1.00  0.00              
ATOM    220  O   TRP   126     -13.415  -8.255  -8.239  1.00  0.00              
ATOM    221  N   ARG   131     -19.842  -8.585 -10.337  1.00  0.00              
ATOM    222  CA  ARG   131     -18.939  -7.592 -10.978  1.00  0.00              
ATOM    223  C   ARG   131     -19.594  -6.221 -11.101  1.00  0.00              
ATOM    224  O   ARG   131     -20.773  -6.059 -10.852  1.00  0.00              
ATOM    225  N   TYR   132     -18.797  -5.261 -11.483  1.00  0.00              
ATOM    226  CA  TYR   132     -19.303  -3.884 -11.645  1.00  0.00              
ATOM    227  C   TYR   132     -18.618  -3.236 -12.870  1.00  0.00              
ATOM    228  O   TYR   132     -17.549  -2.662 -12.763  1.00  0.00              
ATOM    229  N   LYS   133     -19.249  -3.374 -14.024  1.00  0.00              
ATOM    230  CA  LYS   133     -18.716  -2.817 -15.271  1.00  0.00              
ATOM    231  C   LYS   133     -18.730  -1.286 -15.314  1.00  0.00              
ATOM    232  O   LYS   133     -19.771  -0.670 -15.455  1.00  0.00              
ATOM    233  N   ILE   134     -17.564  -0.700 -15.202  1.00  0.00              
ATOM    234  CA  ILE   134     -17.489   0.788 -15.241  1.00  0.00              
ATOM    235  C   ILE   134     -17.451   1.247 -16.693  1.00  0.00              
ATOM    236  O   ILE   134     -16.393   1.398 -17.274  1.00  0.00              
END
