REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0046AL009_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0046  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0046, Gamma-Adaptin ear domain  
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  
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  1 UNREFINED   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1dyn_A 
ATOM      1  N   THR     5      17.492  12.636   7.698  1.00  0.00              
ATOM      2  CA  THR     5      16.645  13.380   8.598  1.00  0.00              
ATOM      3  C   THR     5      17.464  14.514   9.191  1.00  0.00              
ATOM      4  O   THR     5      18.625  14.310   9.559  1.00  0.00              
ATOM      5  N   ALA     6      16.882  15.708   9.241  1.00  0.00              
ATOM      6  CA  ALA     6      17.557  16.857   9.821  1.00  0.00              
ATOM      7  C   ALA     6      17.373  16.775  11.336  1.00  0.00              
ATOM      8  O   ALA     6      16.261  16.619  11.839  1.00  0.00              
ATOM      9  N   TYR     7      18.481  16.812  12.060  1.00  0.00              
ATOM     10  CA  TYR     7      18.443  16.743  13.508  1.00  0.00              
ATOM     11  C   TYR     7      18.168  18.108  14.142  1.00  0.00              
ATOM     12  O   TYR     7      17.434  18.229  15.143  1.00  0.00              
ATOM     13  N   SER     8      18.708  19.158  13.548  1.00  0.00              
ATOM     14  CA  SER     8      18.499  20.458  14.142  1.00  0.00              
ATOM     15  C   SER     8      19.019  21.511  13.229  1.00  0.00              
ATOM     16  O   SER     8      19.940  21.259  12.465  1.00  0.00              
ATOM     17  N   LYS     9      18.405  22.686  13.322  1.00  0.00              
ATOM     18  CA  LYS     9      18.804  23.853  12.564  1.00  0.00              
ATOM     19  C   LYS     9      18.806  24.942  13.618  1.00  0.00              
ATOM     20  O   LYS     9      17.873  25.026  14.402  1.00  0.00              
ATOM     21  N   ASN    10      19.861  25.744  13.659  1.00  0.00              
ATOM     22  CA  ASN    10      19.943  26.822  14.620  1.00  0.00              
ATOM     23  C   ASN    10      21.216  27.615  14.380  1.00  0.00              
ATOM     24  O   ASN    10      22.128  27.132  13.711  1.00  0.00              
ATOM     25  N   GLY    11      21.271  28.840  14.886  1.00  0.00              
ATOM     26  CA  GLY    11      22.443  29.710  14.743  1.00  0.00              
ATOM     27  C   GLY    11      23.517  29.331  15.770  1.00  0.00              
ATOM     28  O   GLY    11      23.197  28.935  16.879  1.00  0.00              
ATOM     29  N   LEU    12      24.781  29.463  15.400  1.00  0.00              
ATOM     30  CA  LEU    12      25.890  29.226  16.329  1.00  0.00              
ATOM     31  C   LEU    12      26.956  30.249  15.920  1.00  0.00              
ATOM     32  O   LEU    12      26.911  30.736  14.793  1.00  0.00              
ATOM     33  N   LYS    13      27.860  30.636  16.816  1.00  0.00              
ATOM     34  CA  LYS    13      28.931  31.570  16.433  1.00  0.00              
ATOM     35  C   LYS    13      30.181  30.755  16.171  1.00  0.00              
ATOM     36  O   LYS    13      30.508  29.862  16.943  1.00  0.00              
ATOM     37  N   ILE    14      30.828  30.962  15.037  1.00  0.00              
ATOM     38  CA  ILE    14      32.073  30.252  14.811  1.00  0.00              
ATOM     39  C   ILE    14      33.036  31.241  15.428  1.00  0.00              
ATOM     40  O   ILE    14      33.107  32.401  15.019  1.00  0.00              
ATOM     41  N   GLU    15      33.672  30.789  16.498  1.00  0.00              
ATOM     42  CA  GLU    15      34.602  31.573  17.286  1.00  0.00              
ATOM     43  C   GLU    15      36.004  31.694  16.708  1.00  0.00              
ATOM     44  O   GLU    15      36.684  32.691  16.948  1.00  0.00              
ATOM     45  N   SER    26      31.851  35.052  13.590  1.00  0.00              
ATOM     46  CA  SER    26      30.558  35.460  13.072  1.00  0.00              
ATOM     47  C   SER    26      29.536  34.367  13.372  1.00  0.00              
ATOM     48  O   SER    26      29.890  33.227  13.661  1.00  0.00              
ATOM     49  N   VAL    27      28.265  34.725  13.324  1.00  0.00              
ATOM     50  CA  VAL    27      27.213  33.782  13.596  1.00  0.00              
ATOM     51  C   VAL    27      26.804  33.229  12.256  1.00  0.00              
ATOM     52  O   VAL    27      26.723  33.967  11.277  1.00  0.00              
ATOM     53  N   THR    28      26.607  31.917  12.202  1.00  0.00              
ATOM     54  CA  THR    28      26.212  31.232  10.976  1.00  0.00              
ATOM     55  C   THR    28      25.060  30.309  11.321  1.00  0.00              
ATOM     56  O   THR    28      24.892  29.931  12.495  1.00  0.00              
ATOM     57  N   VAL    29      24.296  29.940  10.289  1.00  0.00              
ATOM     58  CA  VAL    29      23.118  29.074  10.418  1.00  0.00              
ATOM     59  C   VAL    29      23.496  27.634  10.144  1.00  0.00              
ATOM     60  O   VAL    29      23.785  27.279   9.003  1.00  0.00              
ATOM     61  N   ILE    30      23.432  26.808  11.186  1.00  0.00              
ATOM     62  CA  ILE    30      23.801  25.393  11.112  1.00  0.00              
ATOM     63  C   ILE    30      22.641  24.436  10.897  1.00  0.00              
ATOM     64  O   ILE    30      21.526  24.658  11.364  1.00  0.00              
ATOM     65  N   THR    31      22.938  23.371  10.165  1.00  0.00              
ATOM     66  CA  THR    31      21.998  22.315   9.846  1.00  0.00              
ATOM     67  C   THR    31      22.729  21.021  10.150  1.00  0.00              
ATOM     68  O   THR    31      23.773  20.731   9.567  1.00  0.00              
ATOM     69  N   ILE    32      22.210  20.256  11.092  1.00  0.00              
ATOM     70  CA  ILE    32      22.856  19.006  11.446  1.00  0.00              
ATOM     71  C   ILE    32      21.999  17.810  11.066  1.00  0.00              
ATOM     72  O   ILE    32      20.792  17.817  11.284  1.00  0.00              
ATOM     73  N   GLN    33      22.630  16.802  10.484  1.00  0.00              
ATOM     74  CA  GLN    33      21.956  15.559  10.127  1.00  0.00              
ATOM     75  C   GLN    33      22.873  14.459  10.688  1.00  0.00              
ATOM     76  O   GLN    33      23.918  14.749  11.303  1.00  0.00              
ATOM     77  N   GLU    39      26.193  14.992   8.068  1.00  0.00              
ATOM     78  CA  GLU    39      26.959  16.237   7.929  1.00  0.00              
ATOM     79  C   GLU    39      26.517  17.370   8.848  1.00  0.00              
ATOM     80  O   GLU    39      25.398  17.381   9.353  1.00  0.00              
ATOM     81  N   LEU    40      27.378  18.375   8.969  1.00  0.00              
ATOM     82  CA  LEU    40      27.089  19.589   9.729  1.00  0.00              
ATOM     83  C   LEU    40      27.425  20.650   8.683  1.00  0.00              
ATOM     84  O   LEU    40      28.555  20.703   8.197  1.00  0.00              
ATOM     85  N   ASP    41      26.412  21.390   8.248  1.00  0.00              
ATOM     86  CA  ASP    41      26.583  22.424   7.235  1.00  0.00              
ATOM     87  C   ASP    41      26.291  23.768   7.872  1.00  0.00              
ATOM     88  O   ASP    41      25.542  23.823   8.841  1.00  0.00              
ATOM     89  N   MET    42      26.910  24.840   7.378  1.00  0.00              
ATOM     90  CA  MET    42      26.614  26.180   7.902  1.00  0.00              
ATOM     91  C   MET    42      26.391  27.138   6.765  1.00  0.00              
ATOM     92  O   MET    42      27.096  27.088   5.758  1.00  0.00              
ATOM     93  N   THR    43      25.359  27.964   6.912  1.00  0.00              
ATOM     94  CA  THR    43      24.969  28.939   5.901  1.00  0.00              
ATOM     95  C   THR    43      25.119  30.347   6.431  1.00  0.00              
ATOM     96  O   THR    43      25.265  30.552   7.632  1.00  0.00              
ATOM     97  N   LYS    53      25.897  28.294   1.404  1.00  0.00              
ATOM     98  CA  LYS    53      26.472  27.347   2.339  1.00  0.00              
ATOM     99  C   LYS    53      27.990  27.537   2.388  1.00  0.00              
ATOM    100  O   LYS    53      28.689  27.297   1.402  1.00  0.00              
ATOM    101  N   THR    54      28.500  27.945   3.545  1.00  0.00              
ATOM    102  CA  THR    54      29.929  28.186   3.687  1.00  0.00              
ATOM    103  C   THR    54      30.673  26.869   3.682  1.00  0.00              
ATOM    104  O   THR    54      31.773  26.776   3.135  1.00  0.00              
ATOM    105  N   PHE    55      30.071  25.846   4.285  1.00  0.00              
ATOM    106  CA  PHE    55      30.715  24.552   4.326  1.00  0.00              
ATOM    107  C   PHE    55      29.809  23.424   4.774  1.00  0.00              
ATOM    108  O   PHE    55      28.767  23.649   5.379  1.00  0.00              
ATOM    109  N   GLN    56      30.227  22.209   4.453  1.00  0.00              
ATOM    110  CA  GLN    56      29.513  21.013   4.841  1.00  0.00              
ATOM    111  C   GLN    56      30.585  20.050   5.306  1.00  0.00              
ATOM    112  O   GLN    56      31.409  19.592   4.518  1.00  0.00              
ATOM    113  N   LEU    57      30.597  19.807   6.611  1.00  0.00              
ATOM    114  CA  LEU    57      31.553  18.922   7.264  1.00  0.00              
ATOM    115  C   LEU    57      30.913  17.573   7.630  1.00  0.00              
ATOM    116  O   LEU    57      29.834  17.520   8.233  1.00  0.00              
ATOM    117  N   GLN    58      31.571  16.487   7.238  1.00  0.00              
ATOM    118  CA  GLN    58      31.097  15.146   7.522  1.00  0.00              
ATOM    119  C   GLN    58      31.173  14.911   9.023  1.00  0.00              
ATOM    120  O   GLN    58      32.098  15.366   9.694  1.00  0.00              
ATOM    121  N   VAL    67      34.391  12.856  13.908  1.00  0.00              
ATOM    122  CA  VAL    67      34.310  14.049  14.730  1.00  0.00              
ATOM    123  C   VAL    67      34.043  13.698  16.180  1.00  0.00              
ATOM    124  O   VAL    67      33.303  12.771  16.468  1.00  0.00              
ATOM    125  N   PRO    68      34.642  14.456  17.085  1.00  0.00              
ATOM    126  CA  PRO    68      34.466  14.267  18.517  1.00  0.00              
ATOM    127  C   PRO    68      34.256  15.695  19.044  1.00  0.00              
ATOM    128  O   PRO    68      34.395  16.663  18.286  1.00  0.00              
ATOM    129  N   ALA    69      33.953  15.850  20.321  1.00  0.00              
ATOM    130  CA  ALA    69      33.687  17.182  20.839  1.00  0.00              
ATOM    131  C   ALA    69      34.402  17.496  22.158  1.00  0.00              
ATOM    132  O   ALA    69      34.403  16.694  23.086  1.00  0.00              
ATOM    133  N   PHE    70      34.975  18.693  22.244  1.00  0.00              
ATOM    134  CA  PHE    70      35.698  19.096  23.430  1.00  0.00              
ATOM    135  C   PHE    70      35.302  20.472  23.911  1.00  0.00              
ATOM    136  O   PHE    70      34.855  21.315  23.132  1.00  0.00              
ATOM    137  N   ASN    71      35.450  20.684  25.214  1.00  0.00              
ATOM    138  CA  ASN    71      35.144  21.963  25.825  1.00  0.00              
ATOM    139  C   ASN    71      36.388  22.794  25.666  1.00  0.00              
ATOM    140  O   ASN    71      37.472  22.355  26.034  1.00  0.00              
ATOM    141  N   GLN    77      30.411  30.871  25.599  1.00  0.00              
ATOM    142  CA  GLN    77      30.687  29.545  26.127  1.00  0.00              
ATOM    143  C   GLN    77      31.063  28.804  24.869  1.00  0.00              
ATOM    144  O   GLN    77      30.318  28.827  23.890  1.00  0.00              
ATOM    145  N   VAL    78      32.281  28.272  24.862  1.00  0.00              
ATOM    146  CA  VAL    78      32.830  27.590  23.703  1.00  0.00              
ATOM    147  C   VAL    78      32.985  26.077  23.819  1.00  0.00              
ATOM    148  O   VAL    78      33.060  25.502  24.918  1.00  0.00              
ATOM    149  N   ILE    79      32.915  25.442  22.655  1.00  0.00              
ATOM    150  CA  ILE    79      33.103  24.016  22.489  1.00  0.00              
ATOM    151  C   ILE    79      33.679  23.891  21.085  1.00  0.00              
ATOM    152  O   ILE    79      33.702  24.854  20.323  1.00  0.00              
ATOM    153  N   LYS    80      34.236  22.749  20.753  1.00  0.00              
ATOM    154  CA  LYS    80      34.830  22.647  19.450  1.00  0.00              
ATOM    155  C   LYS    80      34.735  21.246  18.907  1.00  0.00              
ATOM    156  O   LYS    80      34.639  20.285  19.665  1.00  0.00              
ATOM    157  N   VAL    81      34.739  21.150  17.581  1.00  0.00              
ATOM    158  CA  VAL    81      34.683  19.873  16.880  1.00  0.00              
ATOM    159  C   VAL    81      36.080  19.579  16.359  1.00  0.00              
ATOM    160  O   VAL    81      36.770  20.486  15.918  1.00  0.00              
ATOM    161  N   LEU    82      36.509  18.325  16.458  1.00  0.00              
ATOM    162  CA  LEU    82      37.822  17.919  15.946  1.00  0.00              
ATOM    163  C   LEU    82      37.777  16.489  15.416  1.00  0.00              
ATOM    164  O   LEU    82      37.088  15.633  15.974  1.00  0.00              
ATOM    165  N   ASN    83      38.495  16.249  14.323  1.00  0.00              
ATOM    166  CA  ASN    83      38.557  14.937  13.696  1.00  0.00              
ATOM    167  C   ASN    83      39.543  14.097  14.498  1.00  0.00              
ATOM    168  O   ASN    83      40.706  14.460  14.630  1.00  0.00              
ATOM    169  N   ILE    93      36.984  23.231  14.969  1.00  0.00              
ATOM    170  CA  ILE    93      35.985  24.248  14.637  1.00  0.00              
ATOM    171  C   ILE    93      35.416  24.720  15.983  1.00  0.00              
ATOM    172  O   ILE    93      34.748  23.945  16.688  1.00  0.00              
ATOM    173  N   LYS    94      35.717  25.959  16.357  1.00  0.00              
ATOM    174  CA  LYS    94      35.247  26.519  17.621  1.00  0.00              
ATOM    175  C   LYS    94      33.873  27.122  17.492  1.00  0.00              
ATOM    176  O   LYS    94      33.671  28.046  16.713  1.00  0.00              
ATOM    177  N   LEU    95      32.951  26.656  18.322  1.00  0.00              
ATOM    178  CA  LEU    95      31.568  27.119  18.291  1.00  0.00              
ATOM    179  C   LEU    95      31.256  27.780  19.627  1.00  0.00              
ATOM    180  O   LEU    95      31.721  27.330  20.664  1.00  0.00              
ATOM    181  N   THR    96      30.522  28.886  19.590  1.00  0.00              
ATOM    182  CA  THR    96      30.190  29.617  20.804  1.00  0.00              
ATOM    183  C   THR    96      28.713  29.943  20.936  1.00  0.00              
ATOM    184  O   THR    96      28.010  30.130  19.945  1.00  0.00              
ATOM    185  N   TYR    97      28.273  30.023  22.184  1.00  0.00              
ATOM    186  CA  TYR    97      26.906  30.359  22.540  1.00  0.00              
ATOM    187  C   TYR    97      26.935  31.335  23.706  1.00  0.00              
ATOM    188  O   TYR    97      27.748  31.199  24.623  1.00  0.00              
ATOM    189  N   ASN    98      25.329  28.887  28.602  1.00  0.00              
ATOM    190  CA  ASN    98      25.819  27.536  28.798  1.00  0.00              
ATOM    191  C   ASN    98      24.785  26.488  28.417  1.00  0.00              
ATOM    192  O   ASN    98      25.133  25.453  27.860  1.00  0.00              
ATOM    193  N   HIS    99      23.517  26.733  28.729  1.00  0.00              
ATOM    194  CA  HIS    99      22.472  25.765  28.409  1.00  0.00              
ATOM    195  C   HIS    99      22.303  25.641  26.904  1.00  0.00              
ATOM    196  O   HIS    99      21.889  24.602  26.406  1.00  0.00              
ATOM    197  N   LYS   100      22.625  26.704  26.186  1.00  0.00              
ATOM    198  CA  LYS   100      22.549  26.702  24.729  1.00  0.00              
ATOM    199  C   LYS   100      23.604  25.712  24.198  1.00  0.00              
ATOM    200  O   LYS   100      23.346  24.951  23.260  1.00  0.00              
ATOM    201  N   GLY   101      24.799  25.749  24.793  1.00  0.00              
ATOM    202  CA  GLY   101      25.899  24.861  24.426  1.00  0.00              
ATOM    203  C   GLY   101      25.448  23.446  24.798  1.00  0.00              
ATOM    204  O   GLY   101      25.603  22.506  24.007  1.00  0.00              
ATOM    205  N   SER   102      24.841  23.303  25.975  1.00  0.00              
ATOM    206  CA  SER   102      24.365  22.002  26.444  1.00  0.00              
ATOM    207  C   SER   102      23.260  21.356  25.607  1.00  0.00              
ATOM    208  O   SER   102      23.197  20.131  25.538  1.00  0.00              
ATOM    209  N   ALA   103      22.377  22.156  25.004  1.00  0.00              
ATOM    210  CA  ALA   103      21.341  21.601  24.138  1.00  0.00              
ATOM    211  C   ALA   103      21.983  21.130  22.839  1.00  0.00              
ATOM    212  O   ALA   103      21.647  20.062  22.336  1.00  0.00              
ATOM    213  N   MET   104      22.943  21.895  22.323  1.00  0.00              
ATOM    214  CA  MET   104      23.643  21.510  21.102  1.00  0.00              
ATOM    215  C   MET   104      24.515  20.272  21.284  1.00  0.00              
ATOM    216  O   MET   104      24.681  19.488  20.356  1.00  0.00              
ATOM    217  N   GLN   105      25.079  20.093  22.469  1.00  0.00              
ATOM    218  CA  GLN   105      25.888  18.912  22.747  1.00  0.00              
ATOM    219  C   GLN   105      25.025  17.654  22.676  1.00  0.00              
ATOM    220  O   GLN   105      25.486  16.610  22.245  1.00  0.00              
ATOM    221  N   ASP   106      23.764  17.758  23.089  1.00  0.00              
ATOM    222  CA  ASP   106      22.845  16.617  23.063  1.00  0.00              
ATOM    223  C   ASP   106      22.428  16.275  21.640  1.00  0.00              
ATOM    224  O   ASP   106      22.129  15.120  21.331  1.00  0.00              
ATOM    225  N   LEU   107      22.412  17.284  20.775  1.00  0.00              
ATOM    226  CA  LEU   107      22.058  17.096  19.386  1.00  0.00              
ATOM    227  C   LEU   107      23.204  16.440  18.645  1.00  0.00              
ATOM    228  O   LEU   107      22.967  15.568  17.821  1.00  0.00              
ATOM    229  N   ALA   108      24.439  16.855  18.924  1.00  0.00              
ATOM    230  CA  ALA   108      25.605  16.261  18.277  1.00  0.00              
ATOM    231  C   ALA   108      25.713  14.793  18.623  1.00  0.00              
ATOM    232  O   ALA   108      26.054  14.001  17.769  1.00  0.00              
ATOM    233  N   GLU   109      25.424  14.434  19.876  1.00  0.00              
ATOM    234  CA  GLU   109      25.472  13.027  20.340  1.00  0.00              
ATOM    235  C   GLU   109      24.613  12.166  19.439  1.00  0.00              
ATOM    236  O   GLU   109      24.989  11.052  19.058  1.00  0.00              
ATOM    237  N   VAL   110      23.457  12.730  19.105  1.00  0.00              
ATOM    238  CA  VAL   110      22.445  12.125  18.251  1.00  0.00              
ATOM    239  C   VAL   110      22.971  11.892  16.843  1.00  0.00              
ATOM    240  O   VAL   110      22.493  11.007  16.138  1.00  0.00              
END
