REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0046AL009_2 
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  2 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 7paz 
ATOM      1  N   ILE     4      -7.840  31.288 -16.798  1.00  0.00              
ATOM      2  CA  ILE     4      -7.725  32.368 -15.815  1.00  0.00              
ATOM      3  C   ILE     4      -6.331  32.298 -15.206  1.00  0.00              
ATOM      4  O   ILE     4      -5.916  31.224 -14.767  1.00  0.00              
ATOM      5  N   THR     5      -5.604  33.408 -15.298  1.00  0.00              
ATOM      6  CA  THR     5      -4.222  33.412 -14.814  1.00  0.00              
ATOM      7  C   THR     5      -4.158  33.922 -13.371  1.00  0.00              
ATOM      8  O   THR     5      -4.770  34.940 -13.055  1.00  0.00              
ATOM      9  N   ALA     6      -3.465  33.174 -12.528  1.00  0.00              
ATOM     10  CA  ALA     6      -3.255  33.455 -11.114  1.00  0.00              
ATOM     11  C   ALA     6      -1.764  33.558 -10.789  1.00  0.00              
ATOM     12  O   ALA     6      -1.051  32.598 -11.101  1.00  0.00              
ATOM     13  N   TYR     7      -1.308  34.626 -10.133  1.00  0.00              
ATOM     14  CA  TYR     7       0.104  34.734  -9.763  1.00  0.00              
ATOM     15  C   TYR     7       0.342  34.386  -8.296  1.00  0.00              
ATOM     16  O   TYR     7      -0.426  34.800  -7.434  1.00  0.00              
ATOM     17  N   SER     8       1.423  33.690  -7.983  1.00  0.00              
ATOM     18  CA  SER     8       1.776  33.427  -6.584  1.00  0.00              
ATOM     19  C   SER     8       2.889  34.403  -6.205  1.00  0.00              
ATOM     20  O   SER     8       3.887  34.510  -6.917  1.00  0.00              
ATOM     21  N   LYS     9       2.717  35.225  -5.179  1.00  0.00              
ATOM     22  CA  LYS     9       3.716  36.237  -4.836  1.00  0.00              
ATOM     23  C   LYS     9       4.024  36.321  -3.338  1.00  0.00              
ATOM     24  O   LYS     9       3.149  36.064  -2.510  1.00  0.00              
ATOM     25  N   ASN    10       5.228  36.767  -3.011  1.00  0.00              
ATOM     26  CA  ASN    10       5.699  37.016  -1.661  1.00  0.00              
ATOM     27  C   ASN    10       4.986  38.221  -1.044  1.00  0.00              
ATOM     28  O   ASN    10       4.727  38.235   0.157  1.00  0.00              
ATOM     29  N   THR    17       0.669  35.625  -1.142  1.00  0.00              
ATOM     30  CA  THR    17      -0.694  35.688  -1.646  1.00  0.00              
ATOM     31  C   THR    17      -0.836  35.102  -3.052  1.00  0.00              
ATOM     32  O   THR    17       0.151  35.062  -3.782  1.00  0.00              
ATOM     33  N   PHE    18      -2.069  34.741  -3.362  1.00  0.00              
ATOM     34  CA  PHE    18      -2.570  34.354  -4.666  1.00  0.00              
ATOM     35  C   PHE    18      -3.309  35.598  -5.189  1.00  0.00              
ATOM     36  O   PHE    18      -4.127  36.160  -4.447  1.00  0.00              
ATOM     37  N   GLU    19      -3.008  36.046  -6.403  1.00  0.00              
ATOM     38  CA  GLU    19      -3.742  37.193  -6.967  1.00  0.00              
ATOM     39  C   GLU    19      -4.252  36.765  -8.339  1.00  0.00              
ATOM     40  O   GLU    19      -3.396  36.439  -9.168  1.00  0.00              
ATOM     41  N   ARG    20      -5.538  36.670  -8.601  1.00  0.00              
ATOM     42  CA  ARG    20      -6.620  37.015  -7.662  1.00  0.00              
ATOM     43  C   ARG    20      -6.820  35.879  -6.657  1.00  0.00              
ATOM     44  O   ARG    20      -6.337  34.774  -6.934  1.00  0.00              
ATOM     45  N   SER    21      -7.468  36.100  -5.512  1.00  0.00              
ATOM     46  CA  SER    21      -7.588  35.001  -4.541  1.00  0.00              
ATOM     47  C   SER    21      -9.019  34.478  -4.534  1.00  0.00              
ATOM     48  O   SER    21      -9.351  33.547  -3.812  1.00  0.00              
ATOM     49  N   ASN    22      -9.812  35.116  -5.384  1.00  0.00              
ATOM     50  CA  ASN    22     -11.174  34.715  -5.671  1.00  0.00              
ATOM     51  C   ASN    22     -11.276  34.481  -7.185  1.00  0.00              
ATOM     52  O   ASN    22     -11.035  35.385  -7.981  1.00  0.00              
ATOM     53  N   THR    23     -11.538  33.243  -7.570  1.00  0.00              
ATOM     54  CA  THR    23     -11.592  32.843  -8.974  1.00  0.00              
ATOM     55  C   THR    23     -12.969  32.259  -9.275  1.00  0.00              
ATOM     56  O   THR    23     -13.397  31.290  -8.642  1.00  0.00              
ATOM     57  N   ASN    24     -13.676  32.877 -10.217  1.00  0.00              
ATOM     58  CA  ASN    24     -14.985  32.389 -10.643  1.00  0.00              
ATOM     59  C   ASN    24     -14.790  31.642 -11.958  1.00  0.00              
ATOM     60  O   ASN    24     -14.191  32.181 -12.888  1.00  0.00              
ATOM     61  N   THR    28     -13.227  25.119 -17.773  1.00  0.00              
ATOM     62  CA  THR    28     -12.216  26.179 -17.764  1.00  0.00              
ATOM     63  C   THR    28     -10.878  25.678 -17.246  1.00  0.00              
ATOM     64  O   THR    28     -10.838  24.675 -16.535  1.00  0.00              
ATOM     65  N   VAL    29      -9.800  26.423 -17.490  1.00  0.00              
ATOM     66  CA  VAL    29      -8.528  26.073 -16.881  1.00  0.00              
ATOM     67  C   VAL    29      -8.048  27.241 -16.014  1.00  0.00              
ATOM     68  O   VAL    29      -8.284  28.415 -16.308  1.00  0.00              
ATOM     69  N   ILE    30      -7.332  26.903 -14.938  1.00  0.00              
ATOM     70  CA  ILE    30      -6.755  27.969 -14.119  1.00  0.00              
ATOM     71  C   ILE    30      -5.247  27.797 -14.163  1.00  0.00              
ATOM     72  O   ILE    30      -4.717  26.714 -13.910  1.00  0.00              
ATOM     73  N   THR    31      -4.516  28.851 -14.534  1.00  0.00              
ATOM     74  CA  THR    31      -3.064  28.647 -14.590  1.00  0.00              
ATOM     75  C   THR    31      -2.407  29.464 -13.476  1.00  0.00              
ATOM     76  O   THR    31      -2.587  30.682 -13.450  1.00  0.00              
ATOM     77  N   ILE    32      -1.681  28.747 -12.637  1.00  0.00              
ATOM     78  CA  ILE    32      -0.979  29.310 -11.491  1.00  0.00              
ATOM     79  C   ILE    32       0.480  29.579 -11.842  1.00  0.00              
ATOM     80  O   ILE    32       1.228  28.658 -12.172  1.00  0.00              
ATOM     81  N   GLN    33       0.891  30.836 -11.763  1.00  0.00              
ATOM     82  CA  GLN    33       2.261  31.214 -12.109  1.00  0.00              
ATOM     83  C   GLN    33       3.017  31.787 -10.922  1.00  0.00              
ATOM     84  O   GLN    33       2.709  32.867 -10.426  1.00  0.00              
ATOM     85  N   ALA    34       4.055  31.105 -10.468  1.00  0.00              
ATOM     86  CA  ALA    34       4.806  31.631  -9.319  1.00  0.00              
ATOM     87  C   ALA    34       5.774  32.710  -9.794  1.00  0.00              
ATOM     88  O   ALA    34       6.907  32.379 -10.155  1.00  0.00              
ATOM     89  N   THR    43       9.510  29.767  -4.482  1.00  0.00              
ATOM     90  CA  THR    43       9.208  29.174  -3.201  1.00  0.00              
ATOM     91  C   THR    43       7.725  28.997  -2.940  1.00  0.00              
ATOM     92  O   THR    43       7.280  29.136  -1.801  1.00  0.00              
ATOM     93  N   ASP    44       6.961  28.691  -3.982  1.00  0.00              
ATOM     94  CA  ASP    44       5.516  28.534  -3.880  1.00  0.00              
ATOM     95  C   ASP    44       5.015  27.377  -4.746  1.00  0.00              
ATOM     96  O   ASP    44       5.664  27.002  -5.722  1.00  0.00              
ATOM     97  N   PHE    45       3.855  26.856  -4.367  1.00  0.00              
ATOM     98  CA  PHE    45       3.159  25.798  -5.078  1.00  0.00              
ATOM     99  C   PHE    45       1.656  25.954  -4.842  1.00  0.00              
ATOM    100  O   PHE    45       1.213  26.970  -4.295  1.00  0.00              
ATOM    101  N   VAL    46       0.896  24.990  -5.327  1.00  0.00              
ATOM    102  CA  VAL    46      -0.557  25.007  -5.179  1.00  0.00              
ATOM    103  C   VAL    46      -1.024  23.593  -4.859  1.00  0.00              
ATOM    104  O   VAL    46      -0.538  22.604  -5.416  1.00  0.00              
ATOM    105  N   PHE    47      -1.956  23.443  -3.923  1.00  0.00              
ATOM    106  CA  PHE    47      -2.424  22.113  -3.530  1.00  0.00              
ATOM    107  C   PHE    47      -3.853  22.180  -3.014  1.00  0.00              
ATOM    108  O   PHE    47      -4.265  23.126  -2.337  1.00  0.00              
ATOM    109  N   GLN    48      -4.651  21.167  -3.330  1.00  0.00              
ATOM    110  CA  GLN    48      -6.030  21.194  -2.838  1.00  0.00              
ATOM    111  C   GLN    48      -6.084  20.802  -1.366  1.00  0.00              
ATOM    112  O   GLN    48      -5.301  19.988  -0.877  1.00  0.00              
ATOM    113  N   LYS    53     -10.929  15.367  -8.082  1.00  0.00              
ATOM    114  CA  LYS    53      -9.732  14.685  -7.596  1.00  0.00              
ATOM    115  C   LYS    53      -8.791  15.678  -6.922  1.00  0.00              
ATOM    116  O   LYS    53      -8.747  16.860  -7.274  1.00  0.00              
ATOM    117  N   THR    54      -8.021  15.194  -5.949  1.00  0.00              
ATOM    118  CA  THR    54      -7.092  16.101  -5.267  1.00  0.00              
ATOM    119  C   THR    54      -5.890  16.403  -6.141  1.00  0.00              
ATOM    120  O   THR    54      -5.588  15.691  -7.100  1.00  0.00              
ATOM    121  N   PHE    55      -5.164  17.498  -5.884  1.00  0.00              
ATOM    122  CA  PHE    55      -4.009  17.740  -6.745  1.00  0.00              
ATOM    123  C   PHE    55      -2.911  18.460  -5.988  1.00  0.00              
ATOM    124  O   PHE    55      -3.111  19.121  -4.974  1.00  0.00              
ATOM    125  N   GLN    56      -1.701  18.352  -6.516  1.00  0.00              
ATOM    126  CA  GLN    56      -0.571  19.014  -5.852  1.00  0.00              
ATOM    127  C   GLN    56       0.491  19.337  -6.893  1.00  0.00              
ATOM    128  O   GLN    56       0.925  18.445  -7.629  1.00  0.00              
ATOM    129  N   LEU    57       0.898  20.600  -7.008  1.00  0.00              
ATOM    130  CA  LEU    57       1.890  20.956  -8.023  1.00  0.00              
ATOM    131  C   LEU    57       3.299  20.926  -7.443  1.00  0.00              
ATOM    132  O   LEU    57       3.451  20.776  -6.232  1.00  0.00              
ATOM    133  N   SER    64       4.925  26.034 -12.992  1.00  0.00              
ATOM    134  CA  SER    64       3.677  26.574 -13.530  1.00  0.00              
ATOM    135  C   SER    64       2.679  25.423 -13.461  1.00  0.00              
ATOM    136  O   SER    64       3.025  24.289 -13.805  1.00  0.00              
ATOM    137  N   SER    65       1.454  25.657 -13.011  1.00  0.00              
ATOM    138  CA  SER    65       0.564  24.490 -12.986  1.00  0.00              
ATOM    139  C   SER    65      -0.751  24.848 -13.656  1.00  0.00              
ATOM    140  O   SER    65      -1.308  25.907 -13.388  1.00  0.00              
ATOM    141  N   VAL    66      -1.196  23.980 -14.555  1.00  0.00              
ATOM    142  CA  VAL    66      -2.451  24.247 -15.232  1.00  0.00              
ATOM    143  C   VAL    66      -3.495  23.260 -14.716  1.00  0.00              
ATOM    144  O   VAL    66      -3.373  22.073 -14.990  1.00  0.00              
ATOM    145  N   VAL    67      -4.469  23.787 -13.991  1.00  0.00              
ATOM    146  CA  VAL    67      -5.558  22.996 -13.443  1.00  0.00              
ATOM    147  C   VAL    67      -6.805  23.064 -14.322  1.00  0.00              
ATOM    148  O   VAL    67      -7.253  24.153 -14.709  1.00  0.00              
ATOM    149  N   PRO    68      -7.384  21.897 -14.592  1.00  0.00              
ATOM    150  CA  PRO    68      -8.656  21.798 -15.283  1.00  0.00              
ATOM    151  C   PRO    68      -9.785  21.540 -14.282  1.00  0.00              
ATOM    152  O   PRO    68      -9.795  20.572 -13.529  1.00  0.00              
ATOM    153  N   ALA    69     -10.753  22.445 -14.277  1.00  0.00              
ATOM    154  CA  ALA    69     -11.868  22.378 -13.348  1.00  0.00              
ATOM    155  C   ALA    69     -13.089  21.757 -13.993  1.00  0.00              
ATOM    156  O   ALA    69     -13.551  22.173 -15.055  1.00  0.00              
ATOM    157  N   ILE    75     -18.998  23.557  -7.785  1.00  0.00              
ATOM    158  CA  ILE    75     -18.836  23.613  -6.333  1.00  0.00              
ATOM    159  C   ILE    75     -17.659  24.517  -6.008  1.00  0.00              
ATOM    160  O   ILE    75     -17.143  25.134  -6.944  1.00  0.00              
ATOM    161  N   THR    76     -17.273  24.600  -4.740  1.00  0.00              
ATOM    162  CA  THR    76     -16.174  25.469  -4.335  1.00  0.00              
ATOM    163  C   THR    76     -14.942  24.628  -4.028  1.00  0.00              
ATOM    164  O   THR    76     -15.085  23.483  -3.595  1.00  0.00              
ATOM    165  N   GLN    77     -13.772  25.213  -4.267  1.00  0.00              
ATOM    166  CA  GLN    77     -12.516  24.518  -4.021  1.00  0.00              
ATOM    167  C   GLN    77     -11.671  25.409  -3.122  1.00  0.00              
ATOM    168  O   GLN    77     -11.536  26.586  -3.455  1.00  0.00              
ATOM    169  N   VAL    78     -11.111  24.955  -2.007  1.00  0.00              
ATOM    170  CA  VAL    78     -10.229  25.892  -1.294  1.00  0.00              
ATOM    171  C   VAL    78      -8.809  25.405  -1.562  1.00  0.00              
ATOM    172  O   VAL    78      -8.548  24.215  -1.389  1.00  0.00              
ATOM    173  N   ILE    79      -7.919  26.258  -2.056  1.00  0.00              
ATOM    174  CA  ILE    79      -6.590  25.700  -2.323  1.00  0.00              
ATOM    175  C   ILE    79      -5.564  26.518  -1.553  1.00  0.00              
ATOM    176  O   ILE    79      -5.853  27.622  -1.109  1.00  0.00              
ATOM    177  N   LYS    80      -4.369  25.962  -1.407  1.00  0.00              
ATOM    178  CA  LYS    80      -3.340  26.676  -0.671  1.00  0.00              
ATOM    179  C   LYS    80      -1.975  26.438  -1.320  1.00  0.00              
ATOM    180  O   LYS    80      -1.843  25.534  -2.136  1.00  0.00              
ATOM    181  N   ARG    90      -3.827  31.361   0.499  1.00  0.00              
ATOM    182  CA  ARG    90      -4.919  30.557  -0.026  1.00  0.00              
ATOM    183  C   ARG    90      -5.636  31.239  -1.181  1.00  0.00              
ATOM    184  O   ARG    90      -5.564  32.444  -1.377  1.00  0.00              
ATOM    185  N   MET    91      -6.406  30.446  -1.914  1.00  0.00              
ATOM    186  CA  MET    91      -7.231  31.009  -2.979  1.00  0.00              
ATOM    187  C   MET    91      -8.516  30.190  -2.987  1.00  0.00              
ATOM    188  O   MET    91      -8.499  28.996  -2.695  1.00  0.00              
ATOM    189  N   ARG    92      -9.623  30.839  -3.304  1.00  0.00              
ATOM    190  CA  ARG    92     -10.883  30.105  -3.366  1.00  0.00              
ATOM    191  C   ARG    92     -11.340  30.070  -4.811  1.00  0.00              
ATOM    192  O   ARG    92     -11.378  31.047  -5.555  1.00  0.00              
ATOM    193  N   ILE    93     -11.695  28.866  -5.485  1.00  0.00              
ATOM    194  CA  ILE    93     -12.198  28.750  -6.854  1.00  0.00              
ATOM    195  C   ILE    93     -13.671  28.359  -6.778  1.00  0.00              
ATOM    196  O   ILE    93     -13.970  27.365  -6.107  1.00  0.00              
ATOM    197  N   LYS    94     -14.631  29.159  -7.499  1.00  0.00              
ATOM    198  CA  LYS    94     -16.045  28.818  -7.383  1.00  0.00              
ATOM    199  C   LYS    94     -16.477  28.316  -8.774  1.00  0.00              
ATOM    200  O   LYS    94     -16.462  29.119  -9.719  1.00  0.00              
ATOM    201  N   LEU    95     -16.775  27.039  -8.925  1.00  0.00              
ATOM    202  CA  LEU    95     -17.187  26.530 -10.226  1.00  0.00              
ATOM    203  C   LEU    95     -18.708  26.341 -10.248  1.00  0.00              
ATOM    204  O   LEU    95     -19.192  25.435  -9.573  1.00  0.00              
ATOM    205  N   MET   104     -19.949  25.801  -0.242  1.00  0.00              
ATOM    206  CA  MET   104     -19.296  27.024   0.220  1.00  0.00              
ATOM    207  C   MET   104     -19.428  27.234   1.732  1.00  0.00              
ATOM    208  O   MET   104     -18.418  27.503   2.381  1.00  0.00              
ATOM    209  N   GLN   105     -20.630  27.184   2.287  1.00  0.00              
ATOM    210  CA  GLN   105     -20.888  27.352   3.719  1.00  0.00              
ATOM    211  C   GLN   105     -20.132  26.331   4.566  1.00  0.00              
ATOM    212  O   GLN   105     -19.635  26.615   5.653  1.00  0.00              
ATOM    213  N   ASP   106     -20.030  25.112   4.053  1.00  0.00              
ATOM    214  CA  ASP   106     -19.272  24.102   4.796  1.00  0.00              
ATOM    215  C   ASP   106     -17.804  24.516   4.880  1.00  0.00              
ATOM    216  O   ASP   106     -17.257  24.537   5.979  1.00  0.00              
ATOM    217  N   LEU   107     -17.220  24.885   3.745  1.00  0.00              
ATOM    218  CA  LEU   107     -15.836  25.341   3.710  1.00  0.00              
ATOM    219  C   LEU   107     -15.606  26.528   4.642  1.00  0.00              
ATOM    220  O   LEU   107     -14.588  26.626   5.332  1.00  0.00              
ATOM    221  N   ALA   108     -16.531  27.485   4.606  1.00  0.00              
ATOM    222  CA  ALA   108     -16.342  28.649   5.471  1.00  0.00              
ATOM    223  C   ALA   108     -16.368  28.242   6.944  1.00  0.00              
ATOM    224  O   ALA   108     -15.683  28.865   7.760  1.00  0.00              
ATOM    225  N   GLU   109     -17.094  27.181   7.291  1.00  0.00              
ATOM    226  CA  GLU   109     -17.120  26.733   8.680  1.00  0.00              
ATOM    227  C   GLU   109     -15.973  25.794   9.031  1.00  0.00              
ATOM    228  O   GLU   109     -15.725  25.608  10.228  1.00  0.00              
END
