REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0074AL009_4 
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  4   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 3icb 
ATOM      1  N   LYS   129       8.436   9.466  -5.979  1.00  0.00              
ATOM      2  CA  LYS   129       9.823   9.462  -5.576  1.00  0.00              
ATOM      3  C   LYS   129      10.500  10.788  -5.888  1.00  0.00              
ATOM      4  O   LYS   129      11.335  11.240  -5.085  1.00  0.00              
ATOM      5  N   ALA   130      10.120  11.390  -6.990  1.00  0.00              
ATOM      6  CA  ALA   130      10.667  12.653  -7.479  1.00  0.00              
ATOM      7  C   ALA   130      10.259  13.832  -6.599  1.00  0.00              
ATOM      8  O   ALA   130      11.041  14.803  -6.404  1.00  0.00              
ATOM      9  N   LYS   131       9.085  13.705  -6.027  1.00  0.00              
ATOM     10  CA  LYS   131       8.452  14.646  -5.096  1.00  0.00              
ATOM     11  C   LYS   131       9.149  14.546  -3.729  1.00  0.00              
ATOM     12  O   LYS   131       9.370  15.582  -3.128  1.00  0.00              
ATOM     13  N   TYR   132       9.473  13.317  -3.298  1.00  0.00              
ATOM     14  CA  TYR   132      10.194  13.162  -2.032  1.00  0.00              
ATOM     15  C   TYR   132      11.604  13.764  -2.161  1.00  0.00              
ATOM     16  O   TYR   132      12.097  14.327  -1.177  1.00  0.00              
ATOM     17  N   ASP   133      12.224  13.575  -3.291  1.00  0.00              
ATOM     18  CA  ASP   133      13.572  14.104  -3.498  1.00  0.00              
ATOM     19  C   ASP   133      13.515  15.621  -3.411  1.00  0.00              
ATOM     20  O   ASP   133      14.439  16.301  -2.930  1.00  0.00              
ATOM     21  N   ALA   134      12.396  16.134  -3.813  1.00  0.00              
ATOM     22  CA  ALA   134      12.092  17.578  -3.812  1.00  0.00              
ATOM     23  C   ALA   134      12.081  18.149  -2.387  1.00  0.00              
ATOM     24  O   ALA   134      12.677  19.220  -2.106  1.00  0.00              
ATOM     25  N   ILE   135      11.365  17.474  -1.536  1.00  0.00              
ATOM     26  CA  ILE   135      11.168  17.753  -0.086  1.00  0.00              
ATOM     27  C   ILE   135      12.530  17.546   0.563  1.00  0.00              
ATOM     28  O   ILE   135      13.098  18.466   1.160  1.00  0.00              
ATOM     29  N   PHE   136      13.081  16.336   0.400  1.00  0.00              
ATOM     30  CA  PHE   136      14.426  16.064   0.939  1.00  0.00              
ATOM     31  C   PHE   136      15.316  17.291   0.691  1.00  0.00              
ATOM     32  O   PHE   136      15.913  17.825   1.637  1.00  0.00              
ATOM     33  N   ASP   137      15.421  17.704  -0.548  1.00  0.00              
ATOM     34  CA  ASP   137      16.202  18.783  -1.104  1.00  0.00              
ATOM     35  C   ASP   137      16.078  20.179  -0.543  1.00  0.00              
ATOM     36  O   ASP   137      17.121  20.847  -0.324  1.00  0.00              
ATOM     37  N   SER   138      14.861  20.621  -0.273  1.00  0.00              
ATOM     38  CA  SER   138      14.643  21.946   0.341  1.00  0.00              
ATOM     39  C   SER   138      15.383  22.028   1.673  1.00  0.00              
ATOM     40  O   SER   138      16.006  23.047   1.991  1.00  0.00              
ATOM     41  N   LEU   139      15.292  20.971   2.439  1.00  0.00              
ATOM     42  CA  LEU   139      15.890  20.838   3.760  1.00  0.00              
ATOM     43  C   LEU   139      17.367  20.589   3.769  1.00  0.00              
ATOM     44  O   LEU   139      18.119  21.337   4.438  1.00  0.00              
ATOM     45  N   SER   140      17.876  19.583   3.115  1.00  0.00              
ATOM     46  CA  SER   140      19.323  19.287   3.086  1.00  0.00              
ATOM     47  C   SER   140      20.263  20.477   2.848  1.00  0.00              
ATOM     48  O   SER   140      21.466  20.513   3.289  1.00  0.00              
ATOM     49  N   ASP   149      21.338  16.616  11.710  1.00  0.00              
ATOM     50  CA  ASP   149      20.256  16.182  12.648  1.00  0.00              
ATOM     51  C   ASP   149      19.192  17.300  12.682  1.00  0.00              
ATOM     52  O   ASP   149      18.000  16.979  12.763  1.00  0.00              
ATOM     53  N   LYS   150      19.517  18.570  12.621  1.00  0.00              
ATOM     54  CA  LYS   150      18.629  19.706  12.688  1.00  0.00              
ATOM     55  C   LYS   150      17.628  19.868  11.553  1.00  0.00              
ATOM     56  O   LYS   150      16.458  20.276  11.721  1.00  0.00              
ATOM     57  N   VAL   151      18.199  19.636  10.386  1.00  0.00              
ATOM     58  CA  VAL   151      17.477  19.658   9.100  1.00  0.00              
ATOM     59  C   VAL   151      16.540  18.475   9.026  1.00  0.00              
ATOM     60  O   VAL   151      15.427  18.607   8.514  1.00  0.00              
ATOM     61  N   LYS   152      16.923  17.303   9.524  1.00  0.00              
ATOM     62  CA  LYS   152      16.055  16.134   9.541  1.00  0.00              
ATOM     63  C   LYS   152      14.897  16.422  10.511  1.00  0.00              
ATOM     64  O   LYS   152      13.715  16.089  10.294  1.00  0.00              
ATOM     65  N   PRO   153      15.238  17.083  11.610  1.00  0.00              
ATOM     66  CA  PRO   153      14.198  17.401  12.609  1.00  0.00              
ATOM     67  C   PRO   153      13.143  18.325  12.011  1.00  0.00              
ATOM     68  O   PRO   153      11.924  18.161  12.077  1.00  0.00              
ATOM     69  N   VAL   154      13.678  19.315  11.368  1.00  0.00              
ATOM     70  CA  VAL   154      12.934  20.398  10.657  1.00  0.00              
ATOM     71  C   VAL   154      12.053  19.764   9.599  1.00  0.00              
ATOM     72  O   VAL   154      10.824  20.018   9.432  1.00  0.00              
ATOM     73  N   LEU   155      12.637  18.839   8.820  1.00  0.00              
ATOM     74  CA  LEU   155      11.863  18.199   7.775  1.00  0.00              
ATOM     75  C   LEU   155      10.680  17.449   8.329  1.00  0.00              
ATOM     76  O   LEU   155       9.583  17.601   7.851  1.00  0.00              
ATOM     77  N   LEU   156      11.022  16.621   9.290  1.00  0.00              
ATOM     78  CA  LEU   156      10.123  15.705   9.973  1.00  0.00              
ATOM     79  C   LEU   156       8.982  16.410  10.652  1.00  0.00              
ATOM     80  O   LEU   156       7.791  16.019  10.491  1.00  0.00              
ATOM     81  N   ASN   157       9.289  17.438  11.437  1.00  0.00              
ATOM     82  CA  ASN   157       8.124  18.074  12.087  1.00  0.00              
ATOM     83  C   ASN   157       7.273  18.810  11.093  1.00  0.00              
ATOM     84  O   ASN   157       6.026  18.613  11.226  1.00  0.00              
ATOM     85  N   SER   158       7.815  19.548  10.128  1.00  0.00              
ATOM     86  CA  SER   158       6.931  20.285   9.172  1.00  0.00              
ATOM     87  C   SER   158       6.146  19.393   8.220  1.00  0.00              
ATOM     88  O   SER   158       4.932  19.549   8.008  1.00  0.00              
ATOM     89  N   LYS   159       6.831  18.454   7.593  1.00  0.00              
ATOM     90  CA  LYS   159       6.303  17.520   6.604  1.00  0.00              
ATOM     91  C   LYS   159       5.771  16.240   7.154  1.00  0.00              
ATOM     92  O   LYS   159       4.600  15.943   6.795  1.00  0.00              
ATOM     93  N   PRO   161      14.354  11.524  17.969  1.00  0.00              
ATOM     94  CA  PRO   161      14.981  12.040  16.745  1.00  0.00              
ATOM     95  C   PRO   161      16.437  11.587  16.685  1.00  0.00              
ATOM     96  O   PRO   161      16.899  11.188  15.602  1.00  0.00              
ATOM     97  N   VAL   162      17.066  11.650  17.823  1.00  0.00              
ATOM     98  CA  VAL   162      18.457  11.262  17.981  1.00  0.00              
ATOM     99  C   VAL   162      18.644   9.813  17.497  1.00  0.00              
ATOM    100  O   VAL   162      19.605   9.558  16.772  1.00  0.00              
ATOM    101  N   ASP   163      17.733   8.970  17.972  1.00  0.00              
ATOM    102  CA  ASP   163      17.771   7.531  17.671  1.00  0.00              
ATOM    103  C   ASP   163      17.411   7.233  16.233  1.00  0.00              
ATOM    104  O   ASP   163      17.941   6.278  15.624  1.00  0.00              
ATOM    105  N   ILE   164      16.588   8.085  15.643  1.00  0.00              
ATOM    106  CA  ILE   164      16.221   7.943  14.209  1.00  0.00              
ATOM    107  C   ILE   164      17.476   8.324  13.411  1.00  0.00              
ATOM    108  O   ILE   164      17.866   7.682  12.462  1.00  0.00              
ATOM    109  N   LEU   165      18.131   9.384  13.833  1.00  0.00              
ATOM    110  CA  LEU   165      19.374   9.863  13.264  1.00  0.00              
ATOM    111  C   LEU   165      20.440   8.776  13.221  1.00  0.00              
ATOM    112  O   LEU   165      21.137   8.590  12.210  1.00  0.00              
ATOM    113  N   GLY   166      20.650   8.048  14.295  1.00  0.00              
ATOM    114  CA  GLY   166      21.670   6.996  14.325  1.00  0.00              
ATOM    115  C   GLY   166      21.371   5.897  13.312  1.00  0.00              
ATOM    116  O   GLY   166      22.236   5.346  12.638  1.00  0.00              
ATOM    117  N   ARG   167      20.111   5.520  13.293  1.00  0.00              
ATOM    118  CA  ARG   167      19.608   4.454  12.431  1.00  0.00              
ATOM    119  C   ARG   167      19.874   4.857  10.992  1.00  0.00              
ATOM    120  O   ARG   167      20.418   4.106  10.191  1.00  0.00              
ATOM    121  N   VAL   168      19.474   6.094  10.706  1.00  0.00              
ATOM    122  CA  VAL   168      19.653   6.602   9.347  1.00  0.00              
ATOM    123  C   VAL   168      21.121   6.836   9.027  1.00  0.00              
ATOM    124  O   VAL   168      21.529   6.385   7.930  1.00  0.00              
ATOM    125  N   PHE   185      20.356  11.157   0.475  1.00  0.00              
ATOM    126  CA  PHE   185      19.049  10.776  -0.045  1.00  0.00              
ATOM    127  C   PHE   185      18.856   9.270  -0.023  1.00  0.00              
ATOM    128  O   PHE   185      17.734   8.809   0.208  1.00  0.00              
ATOM    129  N   ALA   186      19.910   8.542  -0.317  1.00  0.00              
ATOM    130  CA  ALA   186      19.933   7.086  -0.327  1.00  0.00              
ATOM    131  C   ALA   186      19.675   6.551   1.089  1.00  0.00              
ATOM    132  O   ALA   186      18.924   5.550   1.185  1.00  0.00              
ATOM    133  N   VAL   187      20.297   7.165   2.105  1.00  0.00              
ATOM    134  CA  VAL   187      20.119   6.791   3.503  1.00  0.00              
ATOM    135  C   VAL   187      18.673   7.053   3.950  1.00  0.00              
ATOM    136  O   VAL   187      18.058   6.306   4.704  1.00  0.00              
ATOM    137  N   ALA   188      18.144   8.144   3.454  1.00  0.00              
ATOM    138  CA  ALA   188      16.786   8.619   3.695  1.00  0.00              
ATOM    139  C   ALA   188      15.788   7.590   3.204  1.00  0.00              
ATOM    140  O   ALA   188      14.735   7.413   3.782  1.00  0.00              
ATOM    141  N   MET   189      16.128   6.855   2.171  1.00  0.00              
ATOM    142  CA  MET   189      15.191   5.837   1.615  1.00  0.00              
ATOM    143  C   MET   189      14.664   4.968   2.723  1.00  0.00              
ATOM    144  O   MET   189      13.423   4.853   2.770  1.00  0.00              
ATOM    145  N   PHE   190      15.351   4.409   3.665  1.00  0.00              
ATOM    146  CA  PHE   190      14.706   3.638   4.764  1.00  0.00              
ATOM    147  C   PHE   190      13.328   4.165   5.208  1.00  0.00              
ATOM    148  O   PHE   190      12.263   3.472   5.151  1.00  0.00              
ATOM    149  N   LEU   191      13.215   5.335   5.764  1.00  0.00              
ATOM    150  CA  LEU   191      12.052   6.041   6.279  1.00  0.00              
ATOM    151  C   LEU   191      10.890   6.105   5.298  1.00  0.00              
ATOM    152  O   LEU   191       9.681   6.097   5.578  1.00  0.00              
ATOM    153  N   VAL   192      11.275   6.307   4.036  1.00  0.00              
ATOM    154  CA  VAL   192      10.290   6.479   2.948  1.00  0.00              
ATOM    155  C   VAL   192       9.156   5.471   3.074  1.00  0.00              
ATOM    156  O   VAL   192       8.014   5.796   2.723  1.00  0.00              
ATOM    157  N   TYR   193       9.466   4.288   3.504  1.00  0.00              
ATOM    158  CA  TYR   193       8.470   3.191   3.632  1.00  0.00              
ATOM    159  C   TYR   193       7.381   3.587   4.596  1.00  0.00              
ATOM    160  O   TYR   193       6.183   3.372   4.392  1.00  0.00              
ATOM    161  N   CYS   194       7.807   4.238   5.669  1.00  0.00              
ATOM    162  CA  CYS   194       6.896   4.744   6.716  1.00  0.00              
ATOM    163  C   CYS   194       6.168   5.975   6.216  1.00  0.00              
ATOM    164  O   CYS   194       4.992   6.183   6.524  1.00  0.00              
ATOM    165  N   ALA   195       6.873   6.788   5.443  1.00  0.00              
ATOM    166  CA  ALA   195       6.347   8.025   4.842  1.00  0.00              
ATOM    167  C   ALA   195       5.195   7.698   3.874  1.00  0.00              
ATOM    168  O   ALA   195       4.077   8.267   3.912  1.00  0.00              
ATOM    169  N   LEU   196       5.495   6.750   2.999  1.00  0.00              
ATOM    170  CA  LEU   196       4.597   6.256   1.954  1.00  0.00              
ATOM    171  C   LEU   196       3.451   5.450   2.550  1.00  0.00              
ATOM    172  O   LEU   196       2.382   5.288   1.936  1.00  0.00              
END
