REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0074AL009_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0074  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0074, the second EH domain of eps15  
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 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  2 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 5pal 
ATOM      1  N   LYS   129     -26.564  23.085   7.124  1.00  0.00              
ATOM      2  CA  LYS   129     -25.161  23.331   6.847  1.00  0.00              
ATOM      3  C   LYS   129     -24.493  24.053   8.019  1.00  0.00              
ATOM      4  O   LYS   129     -23.371  23.762   8.458  1.00  0.00              
ATOM      5  N   ALA   130     -25.228  24.975   8.646  1.00  0.00              
ATOM      6  CA  ALA   130     -24.670  25.703   9.769  1.00  0.00              
ATOM      7  C   ALA   130     -24.547  24.826  11.013  1.00  0.00              
ATOM      8  O   ALA   130     -23.637  25.046  11.808  1.00  0.00              
ATOM      9  N   LYS   131     -25.403  23.822  11.216  1.00  0.00              
ATOM     10  CA  LYS   131     -25.248  22.881  12.328  1.00  0.00              
ATOM     11  C   LYS   131     -24.061  21.941  12.063  1.00  0.00              
ATOM     12  O   LYS   131     -23.271  21.647  12.968  1.00  0.00              
ATOM     13  N   TYR   132     -23.875  21.473  10.819  1.00  0.00              
ATOM     14  CA  TYR   132     -22.743  20.605  10.498  1.00  0.00              
ATOM     15  C   TYR   132     -21.449  21.353  10.724  1.00  0.00              
ATOM     16  O   TYR   132     -20.491  20.792  11.265  1.00  0.00              
ATOM     17  N   ASP   133     -21.382  22.649  10.384  1.00  0.00              
ATOM     18  CA  ASP   133     -20.142  23.397  10.558  1.00  0.00              
ATOM     19  C   ASP   133     -19.861  23.713  12.021  1.00  0.00              
ATOM     20  O   ASP   133     -18.705  23.712  12.440  1.00  0.00              
ATOM     21  N   ALA   134     -20.907  23.758  12.864  1.00  0.00              
ATOM     22  CA  ALA   134     -20.748  23.848  14.306  1.00  0.00              
ATOM     23  C   ALA   134     -20.022  22.577  14.803  1.00  0.00              
ATOM     24  O   ALA   134     -19.079  22.614  15.606  1.00  0.00              
ATOM     25  N   ILE   135     -20.415  21.377  14.330  1.00  0.00              
ATOM     26  CA  ILE   135     -19.723  20.145  14.716  1.00  0.00              
ATOM     27  C   ILE   135     -18.293  20.184  14.210  1.00  0.00              
ATOM     28  O   ILE   135     -17.355  19.827  14.941  1.00  0.00              
ATOM     29  N   PHE   136     -18.089  20.671  12.984  1.00  0.00              
ATOM     30  CA  PHE   136     -16.758  20.753  12.414  1.00  0.00              
ATOM     31  C   PHE   136     -15.878  21.583  13.336  1.00  0.00              
ATOM     32  O   PHE   136     -14.779  21.141  13.672  1.00  0.00              
ATOM     33  N   ASP   137     -16.360  22.738  13.803  1.00  0.00              
ATOM     34  CA  ASP   137     -15.587  23.586  14.688  1.00  0.00              
ATOM     35  C   ASP   137     -15.205  22.898  15.990  1.00  0.00              
ATOM     36  O   ASP   137     -14.108  23.118  16.481  1.00  0.00              
ATOM     37  N   SER   138     -16.024  22.037  16.599  1.00  0.00              
ATOM     38  CA  SER   138     -15.578  21.318  17.797  1.00  0.00              
ATOM     39  C   SER   138     -14.461  20.320  17.462  1.00  0.00              
ATOM     40  O   SER   138     -13.531  20.100  18.241  1.00  0.00              
ATOM     41  N   LEU   139     -14.506  19.665  16.301  1.00  0.00              
ATOM     42  CA  LEU   139     -13.482  18.683  15.952  1.00  0.00              
ATOM     43  C   LEU   139     -12.125  19.296  15.595  1.00  0.00              
ATOM     44  O   LEU   139     -11.069  18.684  15.757  1.00  0.00              
ATOM     45  N   PHE   145      -8.880  23.474   9.671  1.00  0.00              
ATOM     46  CA  PHE   145      -8.855  22.161   9.028  1.00  0.00              
ATOM     47  C   PHE   145      -8.810  21.072  10.079  1.00  0.00              
ATOM     48  O   PHE   145      -8.297  21.328  11.176  1.00  0.00              
ATOM     49  N   LEU   146      -9.311  19.879   9.793  1.00  0.00              
ATOM     50  CA  LEU   146      -9.119  18.741  10.661  1.00  0.00              
ATOM     51  C   LEU   146      -7.915  18.016  10.081  1.00  0.00              
ATOM     52  O   LEU   146      -7.962  17.412   8.984  1.00  0.00              
ATOM     53  N   LYS   152      -4.737  15.224  10.283  1.00  0.00              
ATOM     54  CA  LYS   152      -4.731  13.798  10.559  1.00  0.00              
ATOM     55  C   LYS   152      -4.709  13.473  12.056  1.00  0.00              
ATOM     56  O   LYS   152      -5.436  12.614  12.547  1.00  0.00              
ATOM     57  N   PRO   153      -3.958  14.274  12.816  1.00  0.00              
ATOM     58  CA  PRO   153      -3.853  14.120  14.252  1.00  0.00              
ATOM     59  C   PRO   153      -5.221  14.295  14.890  1.00  0.00              
ATOM     60  O   PRO   153      -5.588  13.545  15.797  1.00  0.00              
ATOM     61  N   VAL   154      -6.016  15.265  14.457  1.00  0.00              
ATOM     62  CA  VAL   154      -7.353  15.463  14.986  1.00  0.00              
ATOM     63  C   VAL   154      -8.346  14.446  14.445  1.00  0.00              
ATOM     64  O   VAL   154      -9.328  14.135  15.121  1.00  0.00              
ATOM     65  N   LEU   155      -8.155  13.922  13.231  1.00  0.00              
ATOM     66  CA  LEU   155      -9.030  12.878  12.701  1.00  0.00              
ATOM     67  C   LEU   155      -8.931  11.627  13.566  1.00  0.00              
ATOM     68  O   LEU   155      -9.935  10.948  13.801  1.00  0.00              
ATOM     69  N   LEU   156      -7.720  11.362  14.076  1.00  0.00              
ATOM     70  CA  LEU   156      -7.479  10.241  14.968  1.00  0.00              
ATOM     71  C   LEU   156      -8.323  10.391  16.233  1.00  0.00              
ATOM     72  O   LEU   156      -8.807   9.408  16.799  1.00  0.00              
ATOM     73  N   SER   158      -4.513   3.789  12.384  1.00  0.00              
ATOM     74  CA  SER   158      -4.042   4.480  11.194  1.00  0.00              
ATOM     75  C   SER   158      -4.811   4.046   9.964  1.00  0.00              
ATOM     76  O   SER   158      -5.084   4.882   9.100  1.00  0.00              
ATOM     77  N   LYS   159      -5.285   2.799   9.887  1.00  0.00              
ATOM     78  CA  LYS   159      -6.049   2.377   8.723  1.00  0.00              
ATOM     79  C   LYS   159      -7.374   3.131   8.663  1.00  0.00              
ATOM     80  O   LYS   159      -7.808   3.595   7.605  1.00  0.00              
ATOM     81  N   LEU   160      -7.995   3.338   9.825  1.00  0.00              
ATOM     82  CA  LEU   160      -9.255   4.067   9.890  1.00  0.00              
ATOM     83  C   LEU   160      -9.075   5.561   9.571  1.00  0.00              
ATOM     84  O   LEU   160      -9.894   6.167   8.880  1.00  0.00              
ATOM     85  N   PRO   161      -7.971   6.151  10.020  1.00  0.00              
ATOM     86  CA  PRO   161      -7.691   7.546   9.735  1.00  0.00              
ATOM     87  C   PRO   161      -7.426   7.733   8.236  1.00  0.00              
ATOM     88  O   PRO   161      -8.000   8.621   7.601  1.00  0.00              
ATOM     89  N   VAL   162      -6.629   6.859   7.615  1.00  0.00              
ATOM     90  CA  VAL   162      -6.376   6.921   6.167  1.00  0.00              
ATOM     91  C   VAL   162      -7.647   6.747   5.353  1.00  0.00              
ATOM     92  O   VAL   162      -7.843   7.447   4.368  1.00  0.00              
ATOM     93  N   ASP   163      -8.568   5.870   5.765  1.00  0.00              
ATOM     94  CA  ASP   163      -9.808   5.700   5.045  1.00  0.00              
ATOM     95  C   ASP   163     -10.627   6.983   5.094  1.00  0.00              
ATOM     96  O   ASP   163     -11.268   7.346   4.105  1.00  0.00              
ATOM     97  N   ILE   164     -10.612   7.742   6.205  1.00  0.00              
ATOM     98  CA  ILE   164     -11.345   9.003   6.236  1.00  0.00              
ATOM     99  C   ILE   164     -10.746   9.990   5.254  1.00  0.00              
ATOM    100  O   ILE   164     -11.506  10.680   4.576  1.00  0.00              
ATOM    101  N   LEU   165      -9.413  10.053   5.126  1.00  0.00              
ATOM    102  CA  LEU   165      -8.813  10.930   4.112  1.00  0.00              
ATOM    103  C   LEU   165      -9.128  10.428   2.710  1.00  0.00              
ATOM    104  O   LEU   165      -9.479  11.220   1.830  1.00  0.00              
ATOM    105  N   GLY   166      -9.118   9.117   2.482  1.00  0.00              
ATOM    106  CA  GLY   166      -9.460   8.550   1.184  1.00  0.00              
ATOM    107  C   GLY   166     -10.859   8.949   0.714  1.00  0.00              
ATOM    108  O   GLY   166     -11.092   9.344  -0.439  1.00  0.00              
ATOM    109  N   ARG   167     -11.805   8.972   1.640  1.00  0.00              
ATOM    110  CA  ARG   167     -13.173   9.336   1.333  1.00  0.00              
ATOM    111  C   ARG   167     -13.457  10.827   1.343  1.00  0.00              
ATOM    112  O   ARG   167     -14.355  11.255   0.611  1.00  0.00              
ATOM    113  N   VAL   168     -12.748  11.641   2.115  1.00  0.00              
ATOM    114  CA  VAL   168     -13.146  13.029   2.264  1.00  0.00              
ATOM    115  C   VAL   168     -12.200  14.082   1.743  1.00  0.00              
ATOM    116  O   VAL   168     -12.631  15.218   1.505  1.00  0.00              
ATOM    117  N   PHE   185      -8.892  17.642   6.274  1.00  0.00              
ATOM    118  CA  PHE   185     -10.293  17.838   5.933  1.00  0.00              
ATOM    119  C   PHE   185     -10.745  19.259   6.232  1.00  0.00              
ATOM    120  O   PHE   185     -10.689  19.709   7.371  1.00  0.00              
ATOM    121  N   ALA   186     -11.128  19.996   5.207  1.00  0.00              
ATOM    122  CA  ALA   186     -11.651  21.333   5.389  1.00  0.00              
ATOM    123  C   ALA   186     -13.134  21.275   5.691  1.00  0.00              
ATOM    124  O   ALA   186     -13.781  20.238   5.582  1.00  0.00              
ATOM    125  N   VAL   187     -13.712  22.423   6.025  1.00  0.00              
ATOM    126  CA  VAL   187     -15.119  22.517   6.373  1.00  0.00              
ATOM    127  C   VAL   187     -16.061  22.070   5.274  1.00  0.00              
ATOM    128  O   VAL   187     -17.015  21.335   5.541  1.00  0.00              
ATOM    129  N   ALA   188     -15.868  22.455   4.014  1.00  0.00              
ATOM    130  CA  ALA   188     -16.804  21.998   3.002  1.00  0.00              
ATOM    131  C   ALA   188     -16.534  20.560   2.636  1.00  0.00              
ATOM    132  O   ALA   188     -17.455  19.851   2.217  1.00  0.00              
ATOM    133  N   MET   189     -15.317  20.043   2.820  1.00  0.00              
ATOM    134  CA  MET   189     -15.083  18.613   2.623  1.00  0.00              
ATOM    135  C   MET   189     -15.825  17.814   3.678  1.00  0.00              
ATOM    136  O   MET   189     -16.497  16.836   3.362  1.00  0.00              
ATOM    137  N   PHE   190     -15.818  18.301   4.913  1.00  0.00              
ATOM    138  CA  PHE   190     -16.533  17.654   5.997  1.00  0.00              
ATOM    139  C   PHE   190     -18.033  17.673   5.726  1.00  0.00              
ATOM    140  O   PHE   190     -18.718  16.659   5.897  1.00  0.00              
ATOM    141  N   LEU   191     -18.574  18.808   5.295  1.00  0.00              
ATOM    142  CA  LEU   191     -19.999  18.900   5.002  1.00  0.00              
ATOM    143  C   LEU   191     -20.410  17.919   3.894  1.00  0.00              
ATOM    144  O   LEU   191     -21.499  17.329   3.898  1.00  0.00              
ATOM    145  N   VAL   192     -19.520  17.730   2.908  1.00  0.00              
ATOM    146  CA  VAL   192     -19.756  16.779   1.818  1.00  0.00              
ATOM    147  C   VAL   192     -19.817  15.353   2.316  1.00  0.00              
ATOM    148  O   VAL   192     -20.721  14.626   1.894  1.00  0.00              
ATOM    149  N   TYR   193     -18.880  14.991   3.205  1.00  0.00              
ATOM    150  CA  TYR   193     -18.867  13.660   3.771  1.00  0.00              
ATOM    151  C   TYR   193     -20.159  13.394   4.496  1.00  0.00              
ATOM    152  O   TYR   193     -20.746  12.334   4.308  1.00  0.00              
ATOM    153  N   CYS   194     -20.666  14.352   5.284  1.00  0.00              
ATOM    154  CA  CYS   194     -21.949  14.166   5.950  1.00  0.00              
ATOM    155  C   CYS   194     -23.070  14.037   4.903  1.00  0.00              
ATOM    156  O   CYS   194     -23.974  13.202   5.044  1.00  0.00              
ATOM    157  N   ALA   195     -23.044  14.806   3.812  1.00  0.00              
ATOM    158  CA  ALA   195     -24.085  14.755   2.788  1.00  0.00              
ATOM    159  C   ALA   195     -24.136  13.414   2.064  1.00  0.00              
ATOM    160  O   ALA   195     -25.231  12.900   1.810  1.00  0.00              
ATOM    161  N   LEU   196     -22.988  12.790   1.827  1.00  0.00              
ATOM    162  CA  LEU   196     -22.952  11.529   1.125  1.00  0.00              
ATOM    163  C   LEU   196     -23.132  10.270   1.946  1.00  0.00              
ATOM    164  O   LEU   196     -23.156   9.169   1.364  1.00  0.00              
END
