REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0046AL009_4 
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  4   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1msp_A 
ATOM      1  N   ILE     4      11.276  -8.915  16.938  1.00  0.00              
ATOM      2  CA  ILE     4      12.517  -8.216  16.732  1.00  0.00              
ATOM      3  C   ILE     4      13.357  -8.290  18.002  1.00  0.00              
ATOM      4  O   ILE     4      12.864  -8.347  19.146  1.00  0.00              
ATOM      5  N   THR     5      14.652  -8.212  17.766  1.00  0.00              
ATOM      6  CA  THR     5      15.625  -8.207  18.831  1.00  0.00              
ATOM      7  C   THR     5      16.369  -6.880  18.881  1.00  0.00              
ATOM      8  O   THR     5      16.881  -6.410  17.870  1.00  0.00              
ATOM      9  N   ALA     6      16.423  -6.247  20.051  1.00  0.00              
ATOM     10  CA  ALA     6      17.155  -5.006  20.169  1.00  0.00              
ATOM     11  C   ALA     6      18.242  -5.246  21.176  1.00  0.00              
ATOM     12  O   ALA     6      18.243  -6.206  21.939  1.00  0.00              
ATOM     13  N   TYR     7      19.146  -4.295  21.189  1.00  0.00              
ATOM     14  CA  TYR     7      20.281  -4.270  22.063  1.00  0.00              
ATOM     15  C   TYR     7      20.594  -2.833  22.388  1.00  0.00              
ATOM     16  O   TYR     7      20.942  -2.113  21.438  1.00  0.00              
ATOM     17  N   SER     8      20.501  -2.396  23.676  1.00  0.00              
ATOM     18  CA  SER     8      20.089  -3.145  24.862  1.00  0.00              
ATOM     19  C   SER     8      18.705  -3.718  24.695  1.00  0.00              
ATOM     20  O   SER     8      17.853  -3.172  24.014  1.00  0.00              
ATOM     21  N   LYS    13      16.228  -1.577  28.073  1.00  0.00              
ATOM     22  CA  LYS    13      16.221  -0.165  28.340  1.00  0.00              
ATOM     23  C   LYS    13      17.448   0.575  27.897  1.00  0.00              
ATOM     24  O   LYS    13      18.393   0.030  27.358  1.00  0.00              
ATOM     25  N   ILE    14      17.440   1.853  28.099  1.00  0.00              
ATOM     26  CA  ILE    14      18.609   2.531  27.690  1.00  0.00              
ATOM     27  C   ILE    14      18.933   3.619  28.702  1.00  0.00              
ATOM     28  O   ILE    14      18.034   4.327  29.180  1.00  0.00              
ATOM     29  N   GLU    15      20.224   3.685  29.082  1.00  0.00              
ATOM     30  CA  GLU    15      20.728   4.613  30.082  1.00  0.00              
ATOM     31  C   GLU    15      21.641   5.691  29.584  1.00  0.00              
ATOM     32  O   GLU    15      22.621   5.447  28.907  1.00  0.00              
ATOM     33  N   PHE    16      21.267   6.892  29.930  1.00  0.00              
ATOM     34  CA  PHE    16      22.008   8.056  29.588  1.00  0.00              
ATOM     35  C   PHE    16      22.709   8.432  30.879  1.00  0.00              
ATOM     36  O   PHE    16      22.091   8.473  31.969  1.00  0.00              
ATOM     37  N   THR    17      24.008   8.679  30.764  1.00  0.00              
ATOM     38  CA  THR    17      24.836   9.000  31.918  1.00  0.00              
ATOM     39  C   THR    17      25.200  10.459  31.981  1.00  0.00              
ATOM     40  O   THR    17      25.574  11.012  30.940  1.00  0.00              
ATOM     41  N   ILE    30      24.202   7.891  21.797  1.00  0.00              
ATOM     42  CA  ILE    30      24.332   6.439  21.978  1.00  0.00              
ATOM     43  C   ILE    30      23.950   5.718  20.686  1.00  0.00              
ATOM     44  O   ILE    30      23.833   6.353  19.649  1.00  0.00              
ATOM     45  N   THR    31      23.760   4.393  20.719  1.00  0.00              
ATOM     46  CA  THR    31      23.419   3.627  19.525  1.00  0.00              
ATOM     47  C   THR    31      22.563   2.426  19.884  1.00  0.00              
ATOM     48  O   THR    31      22.656   1.896  20.983  1.00  0.00              
ATOM     49  N   ILE    32      21.713   1.989  18.945  1.00  0.00              
ATOM     50  CA  ILE    32      20.885   0.829  19.167  1.00  0.00              
ATOM     51  C   ILE    32      21.005  -0.105  17.999  1.00  0.00              
ATOM     52  O   ILE    32      21.281   0.319  16.894  1.00  0.00              
ATOM     53  N   GLN    33      20.815  -1.376  18.248  1.00  0.00              
ATOM     54  CA  GLN    33      20.904  -2.378  17.228  1.00  0.00              
ATOM     55  C   GLN    33      19.557  -3.017  17.145  1.00  0.00              
ATOM     56  O   GLN    33      19.009  -3.430  18.172  1.00  0.00              
ATOM     57  N   ALA    34      19.032  -3.069  15.931  1.00  0.00              
ATOM     58  CA  ALA    34      17.758  -3.699  15.741  1.00  0.00              
ATOM     59  C   ALA    34      17.909  -4.808  14.775  1.00  0.00              
ATOM     60  O   ALA    34      18.532  -4.713  13.715  1.00  0.00              
ATOM     61  N   SER    35      17.303  -5.869  15.141  1.00  0.00              
ATOM     62  CA  SER    35      17.413  -6.976  14.264  1.00  0.00              
ATOM     63  C   SER    35      16.077  -7.613  13.975  1.00  0.00              
ATOM     64  O   SER    35      15.252  -7.738  14.855  1.00  0.00              
ATOM     65  N   ASN    36      15.835  -8.007  12.733  1.00  0.00              
ATOM     66  CA  ASN    36      14.570  -8.646  12.440  1.00  0.00              
ATOM     67  C   ASN    36      14.650 -10.126  12.738  1.00  0.00              
ATOM     68  O   ASN    36      15.226 -10.886  11.939  1.00  0.00              
ATOM     69  N   THR    43       9.792  -6.597   7.166  1.00  0.00              
ATOM     70  CA  THR    43       8.951  -5.778   8.017  1.00  0.00              
ATOM     71  C   THR    43       9.414  -4.345   7.823  1.00  0.00              
ATOM     72  O   THR    43      10.470  -4.114   7.295  1.00  0.00              
ATOM     73  N   ASP    44       8.632  -3.375   8.232  1.00  0.00              
ATOM     74  CA  ASP    44       8.977  -1.978   8.112  1.00  0.00              
ATOM     75  C   ASP    44       8.843  -1.498   9.526  1.00  0.00              
ATOM     76  O   ASP    44       8.094  -2.070  10.321  1.00  0.00              
ATOM     77  N   PHE    45       9.586  -0.503   9.870  1.00  0.00              
ATOM     78  CA  PHE    45       9.502  -0.120  11.251  1.00  0.00              
ATOM     79  C   PHE    45       9.725   1.347  11.271  1.00  0.00              
ATOM     80  O   PHE    45      10.278   1.918  10.329  1.00  0.00              
ATOM     81  N   VAL    46       9.257   1.931  12.338  1.00  0.00              
ATOM     82  CA  VAL    46       9.411   3.348  12.528  1.00  0.00              
ATOM     83  C   VAL    46       9.499   3.569  14.026  1.00  0.00              
ATOM     84  O   VAL    46       9.046   2.691  14.757  1.00  0.00              
ATOM     85  N   PHE    47      10.110   4.693  14.441  1.00  0.00              
ATOM     86  CA  PHE    47      10.353   5.047  15.848  1.00  0.00              
ATOM     87  C   PHE    47       9.652   6.301  16.281  1.00  0.00              
ATOM     88  O   PHE    47       9.375   7.189  15.486  1.00  0.00              
ATOM     89  N   GLN    48       9.406   6.358  17.568  1.00  0.00              
ATOM     90  CA  GLN    48       8.773   7.499  18.170  1.00  0.00              
ATOM     91  C   GLN    48       9.457   7.770  19.521  1.00  0.00              
ATOM     92  O   GLN    48       9.851   6.832  20.224  1.00  0.00              
ATOM     93  N   ALA    49       9.621   9.023  19.923  1.00  0.00              
ATOM     94  CA  ALA    49      10.256   9.292  21.213  1.00  0.00              
ATOM     95  C   ALA    49       9.343  10.157  22.021  1.00  0.00              
ATOM     96  O   ALA    49       8.444  10.774  21.466  1.00  0.00              
ATOM     97  N   LEU    57      15.109  14.350  22.619  1.00  0.00              
ATOM     98  CA  LEU    57      15.502  13.108  21.888  1.00  0.00              
ATOM     99  C   LEU    57      15.510  13.191  20.351  1.00  0.00              
ATOM    100  O   LEU    57      14.780  13.932  19.683  1.00  0.00              
ATOM    101  N   GLN    58      16.359  12.381  19.774  1.00  0.00              
ATOM    102  CA  GLN    58      16.447  12.340  18.351  1.00  0.00              
ATOM    103  C   GLN    58      16.904  10.946  17.902  1.00  0.00              
ATOM    104  O   GLN    58      17.615  10.241  18.626  1.00  0.00              
ATOM    105  N   LEU    59      16.456  10.519  16.713  1.00  0.00              
ATOM    106  CA  LEU    59      16.839   9.233  16.189  1.00  0.00              
ATOM    107  C   LEU    59      17.107   9.306  14.732  1.00  0.00              
ATOM    108  O   LEU    59      16.531  10.110  14.008  1.00  0.00              
ATOM    109  N   LEU    60      17.996   8.443  14.324  1.00  0.00              
ATOM    110  CA  LEU    60      18.393   8.419  12.968  1.00  0.00              
ATOM    111  C   LEU    60      19.041   7.101  12.746  1.00  0.00              
ATOM    112  O   LEU    60      19.963   6.728  13.435  1.00  0.00              
ATOM    113  N   SER    61      18.525   6.382  11.792  1.00  0.00              
ATOM    114  CA  SER    61      17.416   6.774  10.980  1.00  0.00              
ATOM    115  C   SER    61      16.178   6.497  11.788  1.00  0.00              
ATOM    116  O   SER    61      16.221   5.699  12.738  1.00  0.00              
ATOM    117  N   PRO    62      15.094   7.155  11.372  1.00  0.00              
ATOM    118  CA  PRO    62      13.757   7.125  11.978  1.00  0.00              
ATOM    119  C   PRO    62      12.796   6.022  11.506  1.00  0.00              
ATOM    120  O   PRO    62      11.773   5.738  12.182  1.00  0.00              
ATOM    121  N   SER    63      13.087   5.392  10.372  1.00  0.00              
ATOM    122  CA  SER    63      12.201   4.322   9.931  1.00  0.00              
ATOM    123  C   SER    63      12.882   3.526   8.884  1.00  0.00              
ATOM    124  O   SER    63      13.962   3.895   8.455  1.00  0.00              
ATOM    125  N   SER    64      12.261   2.438   8.463  1.00  0.00              
ATOM    126  CA  SER    64      12.930   1.673   7.442  1.00  0.00              
ATOM    127  C   SER    64      12.252   0.355   7.286  1.00  0.00              
ATOM    128  O   SER    64      11.159   0.171   7.849  1.00  0.00              
ATOM    129  N   SER    65      12.955  -0.540   6.544  1.00  0.00              
ATOM    130  CA  SER    65      12.584  -1.907   6.189  1.00  0.00              
ATOM    131  C   SER    65      13.757  -2.855   6.365  1.00  0.00              
ATOM    132  O   SER    65      14.805  -2.537   5.863  1.00  0.00              
ATOM    133  N   VAL    66      13.562  -4.012   7.031  1.00  0.00              
ATOM    134  CA  VAL    66      14.562  -5.052   7.290  1.00  0.00              
ATOM    135  C   VAL    66      14.106  -6.387   6.782  1.00  0.00              
ATOM    136  O   VAL    66      13.056  -6.869   7.169  1.00  0.00              
ATOM    137  N   THR    74      19.863  -6.475  10.088  1.00  0.00              
ATOM    138  CA  THR    74      19.927  -5.639  11.258  1.00  0.00              
ATOM    139  C   THR    74      20.309  -4.239  10.930  1.00  0.00              
ATOM    140  O   THR    74      20.915  -3.946   9.915  1.00  0.00              
ATOM    141  N   ILE    75      19.919  -3.373  11.815  1.00  0.00              
ATOM    142  CA  ILE    75      20.237  -2.027  11.584  1.00  0.00              
ATOM    143  C   ILE    75      20.745  -1.402  12.870  1.00  0.00              
ATOM    144  O   ILE    75      20.334  -1.773  13.980  1.00  0.00              
ATOM    145  N   THR    76      21.634  -0.442  12.673  1.00  0.00              
ATOM    146  CA  THR    76      22.254   0.295  13.738  1.00  0.00              
ATOM    147  C   THR    76      21.828   1.726  13.671  1.00  0.00              
ATOM    148  O   THR    76      22.207   2.506  12.787  1.00  0.00              
ATOM    149  N   GLN    77      21.016   2.063  14.641  1.00  0.00              
ATOM    150  CA  GLN    77      20.481   3.378  14.681  1.00  0.00              
ATOM    151  C   GLN    77      20.986   4.246  15.802  1.00  0.00              
ATOM    152  O   GLN    77      21.364   3.758  16.869  1.00  0.00              
ATOM    153  N   VAL    78      20.912   5.557  15.544  1.00  0.00              
ATOM    154  CA  VAL    78      21.387   6.547  16.466  1.00  0.00              
ATOM    155  C   VAL    78      20.446   7.416  17.307  1.00  0.00              
ATOM    156  O   VAL    78      19.717   8.266  16.818  1.00  0.00              
ATOM    157  N   ILE    79      20.565   7.262  18.627  1.00  0.00              
ATOM    158  CA  ILE    79      19.813   8.033  19.589  1.00  0.00              
ATOM    159  C   ILE    79      20.661   9.158  20.210  1.00  0.00              
ATOM    160  O   ILE    79      21.765   8.925  20.667  1.00  0.00              
ATOM    161  N   LYS    80      20.141  10.392  20.234  1.00  0.00              
ATOM    162  CA  LYS    80      20.843  11.522  20.776  1.00  0.00              
ATOM    163  C   LYS    80      20.170  12.163  21.929  1.00  0.00              
ATOM    164  O   LYS    80      19.030  11.874  22.218  1.00  0.00              
ATOM    165  N   VAL    81      20.906  13.039  22.591  1.00  0.00              
ATOM    166  CA  VAL    81      20.390  13.749  23.738  1.00  0.00              
ATOM    167  C   VAL    81      20.927  15.172  23.646  1.00  0.00              
ATOM    168  O   VAL    81      22.068  15.344  23.241  1.00  0.00              
ATOM    169  N   ARG    92      10.876   7.720  26.794  1.00  0.00              
ATOM    170  CA  ARG    92      10.889   6.383  26.197  1.00  0.00              
ATOM    171  C   ARG    92      11.071   6.427  24.709  1.00  0.00              
ATOM    172  O   ARG    92      10.787   7.424  24.073  1.00  0.00              
ATOM    173  N   ILE    93      11.466   5.301  24.151  1.00  0.00              
ATOM    174  CA  ILE    93      11.631   5.177  22.716  1.00  0.00              
ATOM    175  C   ILE    93      10.817   3.987  22.260  1.00  0.00              
ATOM    176  O   ILE    93      11.048   2.883  22.768  1.00  0.00              
ATOM    177  N   LYS    94       9.857   4.196  21.330  1.00  0.00              
ATOM    178  CA  LYS    94       8.992   3.115  20.849  1.00  0.00              
ATOM    179  C   LYS    94       9.323   2.749  19.447  1.00  0.00              
ATOM    180  O   LYS    94       9.527   3.618  18.603  1.00  0.00              
ATOM    181  N   LEU    95       9.376   1.450  19.266  1.00  0.00              
ATOM    182  CA  LEU    95       9.616   0.873  17.979  1.00  0.00              
ATOM    183  C   LEU    95       8.334   0.203  17.517  1.00  0.00              
ATOM    184  O   LEU    95       7.838  -0.732  18.122  1.00  0.00              
ATOM    185  N   THR    96       7.765   0.674  16.440  1.00  0.00              
ATOM    186  CA  THR    96       6.550   0.080  15.968  1.00  0.00              
ATOM    187  C   THR    96       6.873  -0.629  14.691  1.00  0.00              
ATOM    188  O   THR    96       7.647  -0.157  13.880  1.00  0.00              
ATOM    189  N   TYR    97       6.329  -1.773  14.519  1.00  0.00              
ATOM    190  CA  TYR    97       6.613  -2.483  13.295  1.00  0.00              
ATOM    191  C   TYR    97       5.424  -3.291  12.760  1.00  0.00              
ATOM    192  O   TYR    97       4.413  -3.546  13.449  1.00  0.00              
ATOM    193  N   ASN    98       5.575  -3.748  11.536  1.00  0.00              
ATOM    194  CA  ASN    98       4.551  -4.559  10.915  1.00  0.00              
ATOM    195  C   ASN    98       5.127  -5.312   9.723  1.00  0.00              
ATOM    196  O   ASN    98       6.234  -4.972   9.306  1.00  0.00              
ATOM    197  N   HIS    99       4.451  -6.350   9.211  1.00  0.00              
ATOM    198  CA  HIS    99       4.997  -7.086   8.079  1.00  0.00              
ATOM    199  C   HIS    99       4.808  -6.276   6.835  1.00  0.00              
ATOM    200  O   HIS    99       3.761  -5.667   6.707  1.00  0.00              
ATOM    201  N   ASP   106       1.713   4.328   5.183  1.00  0.00              
ATOM    202  CA  ASP   106       0.417   3.736   4.972  1.00  0.00              
ATOM    203  C   ASP   106       0.317   2.319   5.458  1.00  0.00              
ATOM    204  O   ASP   106      -0.752   1.879   5.820  1.00  0.00              
ATOM    205  N   LEU   107       1.421   1.596   5.459  1.00  0.00              
ATOM    206  CA  LEU   107       1.459   0.211   5.917  1.00  0.00              
ATOM    207  C   LEU   107       0.916   0.035   7.334  1.00  0.00              
ATOM    208  O   LEU   107       0.521  -1.066   7.741  1.00  0.00              
ATOM    209  N   ALA   108       0.918   1.131   8.085  1.00  0.00              
ATOM    210  CA  ALA   108       0.454   1.136   9.457  1.00  0.00              
ATOM    211  C   ALA   108      -1.016   1.491   9.580  1.00  0.00              
ATOM    212  O   ALA   108      -1.649   1.160  10.578  1.00  0.00              
ATOM    213  N   GLU   109      -1.543   2.183   8.559  1.00  0.00              
ATOM    214  CA  GLU   109      -2.909   2.661   8.500  1.00  0.00              
ATOM    215  C   GLU   109      -3.929   1.639   8.035  1.00  0.00              
ATOM    216  O   GLU   109      -5.093   1.666   8.412  1.00  0.00              
END
