REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0074AL009_3 
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1iov 
ATOM      1  N   TRP   122      11.558  -3.288  29.084  1.00  0.00              
ATOM      2  CA  TRP   122      12.052  -4.182  30.135  1.00  0.00              
ATOM      3  C   TRP   122      11.588  -5.617  29.893  1.00  0.00              
ATOM      4  O   TRP   122      10.889  -5.917  28.925  1.00  0.00              
ATOM      5  N   ALA   123      12.003  -6.474  30.805  1.00  0.00              
ATOM      6  CA  ALA   123      11.682  -7.895  30.829  1.00  0.00              
ATOM      7  C   ALA   123      11.839  -8.373  32.281  1.00  0.00              
ATOM      8  O   ALA   123      12.989  -8.520  32.749  1.00  0.00              
ATOM      9  N   VAL   124      10.715  -8.591  32.918  1.00  0.00              
ATOM     10  CA  VAL   124      10.720  -9.053  34.313  1.00  0.00              
ATOM     11  C   VAL   124      11.020 -10.544  34.380  1.00  0.00              
ATOM     12  O   VAL   124      10.717 -11.360  33.499  1.00  0.00              
ATOM     13  N   LYS   125      11.640 -10.883  35.497  1.00  0.00              
ATOM     14  CA  LYS   125      12.012 -12.249  35.874  1.00  0.00              
ATOM     15  C   LYS   125      11.729 -12.321  37.384  1.00  0.00              
ATOM     16  O   LYS   125      11.858 -11.301  38.086  1.00  0.00              
ATOM     17  N   PRO   126      11.323 -13.485  37.809  1.00  0.00              
ATOM     18  CA  PRO   126      11.068 -13.776  39.226  1.00  0.00              
ATOM     19  C   PRO   126      12.264 -14.677  39.607  1.00  0.00              
ATOM     20  O   PRO   126      12.988 -15.102  38.686  1.00  0.00              
ATOM     21  N   LYS   129      12.443 -14.899  40.900  1.00  0.00              
ATOM     22  CA  LYS   129      13.562 -15.761  41.320  1.00  0.00              
ATOM     23  C   LYS   129      13.256 -17.200  40.914  1.00  0.00              
ATOM     24  O   LYS   129      14.203 -17.871  40.449  1.00  0.00              
ATOM     25  N   ALA   130      12.016 -17.633  41.044  1.00  0.00              
ATOM     26  CA  ALA   130      11.574 -18.978  40.677  1.00  0.00              
ATOM     27  C   ALA   130      11.741 -19.297  39.189  1.00  0.00              
ATOM     28  O   ALA   130      11.966 -20.494  38.866  1.00  0.00              
ATOM     29  N   LYS   131      11.646 -18.290  38.340  1.00  0.00              
ATOM     30  CA  LYS   131      11.833 -18.526  36.894  1.00  0.00              
ATOM     31  C   LYS   131      13.349 -18.621  36.655  1.00  0.00              
ATOM     32  O   LYS   131      13.828 -19.234  35.699  1.00  0.00              
ATOM     33  N   TYR   132      14.067 -18.039  37.594  1.00  0.00              
ATOM     34  CA  TYR   132      15.520 -17.936  37.657  1.00  0.00              
ATOM     35  C   TYR   132      16.230 -19.225  38.056  1.00  0.00              
ATOM     36  O   TYR   132      17.185 -19.609  37.348  1.00  0.00              
ATOM     37  N   PHE   136      15.342 -15.530  26.402  1.00  0.00              
ATOM     38  CA  PHE   136      16.567 -14.761  26.102  1.00  0.00              
ATOM     39  C   PHE   136      16.326 -14.026  24.781  1.00  0.00              
ATOM     40  O   PHE   136      17.023 -13.081  24.406  1.00  0.00              
ATOM     41  N   ASP   137      15.292 -14.559  24.144  1.00  0.00              
ATOM     42  CA  ASP   137      14.788 -14.069  22.854  1.00  0.00              
ATOM     43  C   ASP   137      14.100 -12.735  23.182  1.00  0.00              
ATOM     44  O   ASP   137      14.071 -11.813  22.387  1.00  0.00              
ATOM     45  N   SER   138      13.578 -12.736  24.390  1.00  0.00              
ATOM     46  CA  SER   138      12.890 -11.600  24.995  1.00  0.00              
ATOM     47  C   SER   138      13.932 -10.515  25.287  1.00  0.00              
ATOM     48  O   SER   138      13.922  -9.438  24.701  1.00  0.00              
ATOM     49  N   LEU   139      14.813 -10.914  26.187  1.00  0.00              
ATOM     50  CA  LEU   139      15.937 -10.145  26.682  1.00  0.00              
ATOM     51  C   LEU   139      16.923  -9.664  25.624  1.00  0.00              
ATOM     52  O   LEU   139      17.533  -8.576  25.812  1.00  0.00              
ATOM     53  N   VAL   154      22.094  -3.794  28.595  1.00  0.00              
ATOM     54  CA  VAL   154      20.866  -3.808  29.374  1.00  0.00              
ATOM     55  C   VAL   154      21.322  -3.661  30.835  1.00  0.00              
ATOM     56  O   VAL   154      22.416  -4.144  31.157  1.00  0.00              
ATOM     57  N   LEU   155      20.533  -2.988  31.625  1.00  0.00              
ATOM     58  CA  LEU   155      20.869  -2.821  33.060  1.00  0.00              
ATOM     59  C   LEU   155      19.800  -3.651  33.799  1.00  0.00              
ATOM     60  O   LEU   155      18.595  -3.447  33.561  1.00  0.00              
ATOM     61  N   LEU   156      20.306  -4.541  34.600  1.00  0.00              
ATOM     62  CA  LEU   156      19.559  -5.501  35.424  1.00  0.00              
ATOM     63  C   LEU   156      19.466  -4.925  36.828  1.00  0.00              
ATOM     64  O   LEU   156      20.514  -4.550  37.372  1.00  0.00              
ATOM     65  N   ASN   157      18.239  -4.871  37.352  1.00  0.00              
ATOM     66  CA  ASN   157      18.077  -4.296  38.688  1.00  0.00              
ATOM     67  C   ASN   157      17.060  -4.912  39.600  1.00  0.00              
ATOM     68  O   ASN   157      15.993  -5.407  39.194  1.00  0.00              
ATOM     69  N   SER   158      17.381  -4.838  40.897  1.00  0.00              
ATOM     70  CA  SER   158      16.450  -5.321  41.931  1.00  0.00              
ATOM     71  C   SER   158      15.212  -4.401  41.824  1.00  0.00              
ATOM     72  O   SER   158      15.319  -3.157  41.794  1.00  0.00              
ATOM     73  N   VAL   162      23.434  -3.965  38.020  1.00  0.00              
ATOM     74  CA  VAL   162      24.611  -4.481  37.294  1.00  0.00              
ATOM     75  C   VAL   162      24.342  -4.310  35.807  1.00  0.00              
ATOM     76  O   VAL   162      23.317  -4.842  35.343  1.00  0.00              
ATOM     77  N   ASP   163      25.195  -3.591  35.135  1.00  0.00              
ATOM     78  CA  ASP   163      25.081  -3.394  33.688  1.00  0.00              
ATOM     79  C   ASP   163      25.672  -4.686  33.066  1.00  0.00              
ATOM     80  O   ASP   163      26.742  -5.177  33.472  1.00  0.00              
ATOM     81  N   ILE   164      24.890  -5.147  32.104  1.00  0.00              
ATOM     82  CA  ILE   164      25.238  -6.361  31.354  1.00  0.00              
ATOM     83  C   ILE   164      25.287  -6.036  29.866  1.00  0.00              
ATOM     84  O   ILE   164      24.322  -5.752  29.148  1.00  0.00              
ATOM     85  N   LEU   165      24.903 -11.823  31.819  1.00  0.00              
ATOM     86  CA  LEU   165      23.595 -11.729  32.455  1.00  0.00              
ATOM     87  C   LEU   165      23.303 -12.618  33.642  1.00  0.00              
ATOM     88  O   LEU   165      22.831 -12.147  34.709  1.00  0.00              
ATOM     89  N   GLY   166      23.526 -13.893  33.485  1.00  0.00              
ATOM     90  CA  GLY   166      23.291 -14.918  34.523  1.00  0.00              
ATOM     91  C   GLY   166      23.769 -14.411  35.874  1.00  0.00              
ATOM     92  O   GLY   166      23.030 -14.481  36.885  1.00  0.00              
ATOM     93  N   ARG   167      24.977 -13.857  35.883  1.00  0.00              
ATOM     94  CA  ARG   167      25.622 -13.282  37.062  1.00  0.00              
ATOM     95  C   ARG   167      24.979 -11.949  37.476  1.00  0.00              
ATOM     96  O   ARG   167      24.847 -11.694  38.684  1.00  0.00              
ATOM     97  N   VAL   168      24.640 -11.143  36.494  1.00  0.00              
ATOM     98  CA  VAL   168      24.024  -9.837  36.797  1.00  0.00              
ATOM     99  C   VAL   168      22.751 -10.109  37.593  1.00  0.00              
ATOM    100  O   VAL   168      22.424  -9.352  38.525  1.00  0.00              
ATOM    101  N   TRP   169      22.097 -11.203  37.201  1.00  0.00              
ATOM    102  CA  TRP   169      20.858 -11.676  37.798  1.00  0.00              
ATOM    103  C   TRP   169      21.050 -12.335  39.162  1.00  0.00              
ATOM    104  O   TRP   169      20.128 -12.184  40.001  1.00  0.00              
ATOM    105  N   GLU   170      22.133 -13.062  39.389  1.00  0.00              
ATOM    106  CA  GLU   170      22.319 -13.721  40.702  1.00  0.00              
ATOM    107  C   GLU   170      22.241 -12.682  41.822  1.00  0.00              
ATOM    108  O   GLU   170      21.520 -12.853  42.808  1.00  0.00              
ATOM    109  N   LEU   171      22.966 -11.620  41.610  1.00  0.00              
ATOM    110  CA  LEU   171      23.164 -10.412  42.400  1.00  0.00              
ATOM    111  C   LEU   171      21.864  -9.672  42.705  1.00  0.00              
ATOM    112  O   LEU   171      21.403  -9.561  43.860  1.00  0.00              
ATOM    113  N   SER   172      21.289  -9.153  41.636  1.00  0.00              
ATOM    114  CA  SER   172      20.005  -8.409  41.696  1.00  0.00              
ATOM    115  C   SER   172      19.030  -9.233  42.537  1.00  0.00              
ATOM    116  O   SER   172      18.266  -8.703  43.349  1.00  0.00              
ATOM    117  N   GLU   184      11.786 -10.564  42.352  1.00  0.00              
ATOM    118  CA  GLU   184      11.248  -9.994  41.103  1.00  0.00              
ATOM    119  C   GLU   184      12.337  -8.967  40.704  1.00  0.00              
ATOM    120  O   GLU   184      12.714  -8.140  41.523  1.00  0.00              
ATOM    121  N   PHE   185      12.833  -9.139  39.508  1.00  0.00              
ATOM    122  CA  PHE   185      13.904  -8.291  38.953  1.00  0.00              
ATOM    123  C   PHE   185      13.527  -7.797  37.572  1.00  0.00              
ATOM    124  O   PHE   185      12.810  -8.471  36.819  1.00  0.00              
ATOM    125  N   ALA   186      13.940  -6.582  37.250  1.00  0.00              
ATOM    126  CA  ALA   186      13.666  -5.958  35.952  1.00  0.00              
ATOM    127  C   ALA   186      15.015  -5.803  35.223  1.00  0.00              
ATOM    128  O   ALA   186      16.018  -5.345  35.773  1.00  0.00              
ATOM    129  N   VAL   187      14.975  -6.289  34.010  1.00  0.00              
ATOM    130  CA  VAL   187      16.034  -6.276  33.020  1.00  0.00              
ATOM    131  C   VAL   187      15.515  -5.249  31.961  1.00  0.00              
ATOM    132  O   VAL   187      14.454  -5.516  31.409  1.00  0.00              
ATOM    133  N   ALA   188      16.297  -4.181  31.812  1.00  0.00              
ATOM    134  CA  ALA   188      15.883  -3.167  30.848  1.00  0.00              
ATOM    135  C   ALA   188      17.018  -2.658  29.993  1.00  0.00              
ATOM    136  O   ALA   188      18.205  -2.773  30.261  1.00  0.00              
ATOM    137  N   MET   189      16.544  -2.048  28.909  1.00  0.00              
ATOM    138  CA  MET   189      17.373  -1.443  27.875  1.00  0.00              
ATOM    139  C   MET   189      18.201  -0.350  28.537  1.00  0.00              
ATOM    140  O   MET   189      17.705   0.353  29.434  1.00  0.00              
END
