REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0072AL009_3 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0072  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0072, CDS domain 1  
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1whi 
ATOM      1  N   ARG    12      16.838  -6.962  40.743  1.00  0.00              
ATOM      2  CA  ARG    12      17.226  -5.945  41.724  1.00  0.00              
ATOM      3  C   ARG    12      17.917  -4.829  40.968  1.00  0.00              
ATOM      4  O   ARG    12      18.752  -5.088  40.108  1.00  0.00              
ATOM      5  N   LEU    13      17.556  -3.593  41.274  1.00  0.00              
ATOM      6  CA  LEU    13      18.141  -2.437  40.601  1.00  0.00              
ATOM      7  C   LEU    13      18.762  -1.482  41.613  1.00  0.00              
ATOM      8  O   LEU    13      18.208  -1.276  42.686  1.00  0.00              
ATOM      9  N   THR    14      19.926  -0.936  41.278  1.00  0.00              
ATOM     10  CA  THR    14      20.581   0.044  42.142  1.00  0.00              
ATOM     11  C   THR    14      19.804   1.331  41.918  1.00  0.00              
ATOM     12  O   THR    14      19.266   1.543  40.834  1.00  0.00              
ATOM     13  N   ARG    15      19.777   2.206  42.912  1.00  0.00              
ATOM     14  CA  ARG    15      19.094   3.484  42.776  1.00  0.00              
ATOM     15  C   ARG    15      20.156   4.579  42.575  1.00  0.00              
ATOM     16  O   ARG    15      21.035   4.771  43.404  1.00  0.00              
ATOM     17  N   GLN    23      16.324   5.618  48.803  1.00  0.00              
ATOM     18  CA  GLN    23      16.286   4.218  48.402  1.00  0.00              
ATOM     19  C   GLN    23      17.663   3.818  47.900  1.00  0.00              
ATOM     20  O   GLN    23      18.327   4.586  47.207  1.00  0.00              
ATOM     21  N   LEU    24      18.081   2.609  48.256  1.00  0.00              
ATOM     22  CA  LEU    24      19.387   2.093  47.875  1.00  0.00              
ATOM     23  C   LEU    24      19.280   0.973  46.831  1.00  0.00              
ATOM     24  O   LEU    24      20.113   0.865  45.925  1.00  0.00              
ATOM     25  N   GLU    25      18.211   0.190  46.910  1.00  0.00              
ATOM     26  CA  GLU    25      18.003  -0.897  45.961  1.00  0.00              
ATOM     27  C   GLU    25      16.523  -1.212  45.919  1.00  0.00              
ATOM     28  O   GLU    25      15.833  -1.098  46.940  1.00  0.00              
ATOM     29  N   VAL    26      16.023  -1.534  44.729  1.00  0.00              
ATOM     30  CA  VAL    26      14.606  -1.885  44.550  1.00  0.00              
ATOM     31  C   VAL    26      14.484  -3.224  43.851  1.00  0.00              
ATOM     32  O   VAL    26      15.432  -3.696  43.207  1.00  0.00              
ATOM     33  N   TYR    27      13.321  -3.838  43.993  1.00  0.00              
ATOM     34  CA  TYR    27      13.043  -5.140  43.417  1.00  0.00              
ATOM     35  C   TYR    27      11.859  -4.951  42.475  1.00  0.00              
ATOM     36  O   TYR    27      10.807  -4.501  42.904  1.00  0.00              
ATOM     37  N   LEU    28      12.058  -5.251  41.195  1.00  0.00              
ATOM     38  CA  LEU    28      11.017  -5.083  40.174  1.00  0.00              
ATOM     39  C   LEU    28       9.783  -5.955  40.347  1.00  0.00              
ATOM     40  O   LEU    28       9.889  -7.155  40.547  1.00  0.00              
ATOM     41  N   LYS    29       8.612  -5.337  40.281  1.00  0.00              
ATOM     42  CA  LYS    29       7.354  -6.053  40.399  1.00  0.00              
ATOM     43  C   LYS    29       6.790  -6.228  39.001  1.00  0.00              
ATOM     44  O   LYS    29       6.452  -7.336  38.599  1.00  0.00              
ATOM     45  N   ASP    30       6.733  -5.134  38.245  1.00  0.00              
ATOM     46  CA  ASP    30       6.213  -5.187  36.879  1.00  0.00              
ATOM     47  C   ASP    30       6.754  -4.044  36.018  1.00  0.00              
ATOM     48  O   ASP    30       7.210  -3.023  36.534  1.00  0.00              
ATOM     49  N   GLY    31       6.749  -4.269  34.706  1.00  0.00              
ATOM     50  CA  GLY    31       7.203  -3.288  33.735  1.00  0.00              
ATOM     51  C   GLY    31       5.944  -2.636  33.190  1.00  0.00              
ATOM     52  O   GLY    31       5.033  -3.320  32.727  1.00  0.00              
ATOM     53  N   VAL    35       9.617   2.391  32.590  1.00  0.00              
ATOM     54  CA  VAL    35       9.222   2.657  33.964  1.00  0.00              
ATOM     55  C   VAL    35       8.767   1.350  34.593  1.00  0.00              
ATOM     56  O   VAL    35       8.034   0.565  33.982  1.00  0.00              
ATOM     57  N   CYS    36       9.256   1.094  35.796  1.00  0.00              
ATOM     58  CA  CYS    36       8.899  -0.107  36.527  1.00  0.00              
ATOM     59  C   CYS    36       8.228   0.271  37.837  1.00  0.00              
ATOM     60  O   CYS    36       8.381   1.382  38.348  1.00  0.00              
ATOM     61  N   SER    37       7.454  -0.674  38.345  1.00  0.00              
ATOM     62  CA  SER    37       6.809  -0.552  39.647  1.00  0.00              
ATOM     63  C   SER    37       7.715  -1.471  40.456  1.00  0.00              
ATOM     64  O   SER    37       8.005  -2.586  40.019  1.00  0.00              
ATOM     65  N   GLN    38       8.176  -1.006  41.615  1.00  0.00              
ATOM     66  CA  GLN    38       9.097  -1.812  42.418  1.00  0.00              
ATOM     67  C   GLN    38       8.897  -1.607  43.909  1.00  0.00              
ATOM     68  O   GLN    38       8.236  -0.658  44.339  1.00  0.00              
ATOM     69  N   SER    39       9.463  -2.516  44.688  1.00  0.00              
ATOM     70  CA  SER    39       9.407  -2.401  46.142  1.00  0.00              
ATOM     71  C   SER    39      10.814  -2.016  46.598  1.00  0.00              
ATOM     72  O   SER    39      11.811  -2.514  46.051  1.00  0.00              
ATOM     73  N   TRP    40      10.900  -1.102  47.562  1.00  0.00              
ATOM     74  CA  TRP    40      12.186  -0.669  48.091  1.00  0.00              
ATOM     75  C   TRP    40      12.738  -1.803  48.936  1.00  0.00              
ATOM     76  O   TRP    40      12.099  -2.247  49.894  1.00  0.00              
ATOM     77  N   GLY    41      13.896  -2.307  48.535  1.00  0.00              
ATOM     78  CA  GLY    41      14.543  -3.419  49.220  1.00  0.00              
ATOM     79  C   GLY    41      15.459  -2.947  50.348  1.00  0.00              
ATOM     80  O   GLY    41      15.541  -3.570  51.414  1.00  0.00              
ATOM     81  N   ARG    42      16.151  -1.845  50.103  1.00  0.00              
ATOM     82  CA  ARG    42      17.067  -1.263  51.076  1.00  0.00              
ATOM     83  C   ARG    42      16.946   0.244  50.950  1.00  0.00              
ATOM     84  O   ARG    42      16.792   0.770  49.851  1.00  0.00              
ATOM     85  N   SER    43      17.033   0.933  52.080  1.00  0.00              
ATOM     86  CA  SER    43      16.914   2.378  52.124  1.00  0.00              
ATOM     87  C   SER    43      17.675   2.907  53.350  1.00  0.00              
ATOM     88  O   SER    43      17.938   2.155  54.290  1.00  0.00              
ATOM     89  N   SER    51       6.205   0.693  47.892  1.00  0.00              
ATOM     90  CA  SER    51       6.132   0.495  46.450  1.00  0.00              
ATOM     91  C   SER    51       6.325   1.850  45.793  1.00  0.00              
ATOM     92  O   SER    51       5.677   2.820  46.171  1.00  0.00              
ATOM     93  N   GLN    52       7.217   1.902  44.809  1.00  0.00              
ATOM     94  CA  GLN    52       7.531   3.137  44.108  1.00  0.00              
ATOM     95  C   GLN    52       7.555   2.870  42.605  1.00  0.00              
ATOM     96  O   GLN    52       7.471   1.721  42.170  1.00  0.00              
ATOM     97  N   ALA    53       7.604   3.945  41.828  1.00  0.00              
ATOM     98  CA  ALA    53       7.730   3.879  40.369  1.00  0.00              
ATOM     99  C   ALA    53       9.133   4.397  40.119  1.00  0.00              
ATOM    100  O   ALA    53       9.568   5.342  40.788  1.00  0.00              
ATOM    101  N   SER    54       9.837   3.819  39.153  1.00  0.00              
ATOM    102  CA  SER    54      11.199   4.249  38.858  1.00  0.00              
ATOM    103  C   SER    54      11.482   4.083  37.369  1.00  0.00              
ATOM    104  O   SER    54      10.963   3.145  36.740  1.00  0.00              
ATOM    105  N   LYS    55      12.272   4.991  36.808  1.00  0.00              
ATOM    106  CA  LYS    55      12.654   4.883  35.403  1.00  0.00              
ATOM    107  C   LYS    55      14.072   4.287  35.329  1.00  0.00              
ATOM    108  O   LYS    55      14.941   4.619  36.139  1.00  0.00              
ATOM    109  N   VAL    56      14.278   3.342  34.416  1.00  0.00              
ATOM    110  CA  VAL    56      15.584   2.709  34.237  1.00  0.00              
ATOM    111  C   VAL    56      16.501   3.663  33.471  1.00  0.00              
ATOM    112  O   VAL    56      16.157   4.121  32.379  1.00  0.00              
ATOM    113  N   CYS    57      17.671   3.958  34.033  1.00  0.00              
ATOM    114  CA  CYS    57      18.594   4.897  33.397  1.00  0.00              
ATOM    115  C   CYS    57      19.912   4.300  32.920  1.00  0.00              
ATOM    116  O   CYS    57      20.642   4.949  32.173  1.00  0.00              
ATOM    117  N   GLN    58      20.225   3.089  33.374  1.00  0.00              
ATOM    118  CA  GLN    58      21.438   2.383  32.979  1.00  0.00              
ATOM    119  C   GLN    58      21.120   0.904  33.001  1.00  0.00              
ATOM    120  O   GLN    58      20.458   0.442  33.916  1.00  0.00              
ATOM    121  N   SER    80      22.073  -2.707  27.594  1.00  0.00              
ATOM    122  CA  SER    80      22.376  -1.599  26.710  1.00  0.00              
ATOM    123  C   SER    80      21.385  -1.384  25.582  1.00  0.00              
ATOM    124  O   SER    80      20.360  -2.074  25.495  1.00  0.00              
ATOM    125  N   ILE    81      21.740  -0.478  24.675  1.00  0.00              
ATOM    126  CA  ILE    81      20.883  -0.122  23.540  1.00  0.00              
ATOM    127  C   ILE    81      21.687   0.034  22.254  1.00  0.00              
ATOM    128  O   ILE    81      22.848   0.477  22.290  1.00  0.00              
ATOM    129  N   ILE    82      21.066  -0.312  21.128  1.00  0.00              
ATOM    130  CA  ILE    82      21.706  -0.161  19.829  1.00  0.00              
ATOM    131  C   ILE    82      21.176   1.171  19.326  1.00  0.00              
ATOM    132  O   ILE    82      19.976   1.411  19.366  1.00  0.00              
ATOM    133  N   CYS    83      22.049   1.995  18.777  1.00  0.00              
ATOM    134  CA  CYS    83      21.643   3.306  18.297  1.00  0.00              
ATOM    135  C   CYS    83      21.552   3.413  16.766  1.00  0.00              
ATOM    136  O   CYS    83      22.175   2.637  16.041  1.00  0.00              
ATOM    137  N   SER    91      24.718   3.362  14.499  1.00  0.00              
ATOM    138  CA  SER    91      25.590   2.200  14.505  1.00  0.00              
ATOM    139  C   SER    91      26.333   1.940  15.808  1.00  0.00              
ATOM    140  O   SER    91      27.064   0.949  15.923  1.00  0.00              
ATOM    141  N   ASN    92      26.193   2.840  16.775  1.00  0.00              
ATOM    142  CA  ASN    92      26.851   2.645  18.051  1.00  0.00              
ATOM    143  C   ASN    92      25.956   1.815  18.949  1.00  0.00              
ATOM    144  O   ASN    92      24.754   1.673  18.695  1.00  0.00              
ATOM    145  N   CYS    93      26.571   1.236  19.970  1.00  0.00              
ATOM    146  CA  CYS    93      25.895   0.427  20.976  1.00  0.00              
ATOM    147  C   CYS    93      26.485   0.907  22.294  1.00  0.00              
ATOM    148  O   CYS    93      27.720   0.986  22.430  1.00  0.00              
ATOM    149  N   SER    94      25.628   1.206  23.254  1.00  0.00              
ATOM    150  CA  SER    94      26.073   1.665  24.563  1.00  0.00              
ATOM    151  C   SER    94      25.501   0.757  25.658  1.00  0.00              
ATOM    152  O   SER    94      24.355   0.329  25.576  1.00  0.00              
ATOM    153  N   HIS    95      26.332   0.372  26.617  1.00  0.00              
ATOM    154  CA  HIS    95      25.849  -0.418  27.752  1.00  0.00              
ATOM    155  C   HIS    95      26.609   0.052  28.988  1.00  0.00              
ATOM    156  O   HIS    95      27.547   0.842  28.886  1.00  0.00              
ATOM    157  N   MET   100      20.511   0.314  36.830  1.00  0.00              
ATOM    158  CA  MET   100      20.144   1.342  37.797  1.00  0.00              
ATOM    159  C   MET   100      18.873   2.079  37.398  1.00  0.00              
ATOM    160  O   MET   100      18.494   2.115  36.222  1.00  0.00              
ATOM    161  N   CYS   101      18.212   2.667  38.387  1.00  0.00              
ATOM    162  CA  CYS   101      16.985   3.411  38.136  1.00  0.00              
ATOM    163  C   CYS   101      16.942   4.651  39.012  1.00  0.00              
ATOM    164  O   CYS   101      17.786   4.825  39.900  1.00  0.00              
ATOM    165  N   HIS   102      15.998   5.536  38.696  1.00  0.00              
ATOM    166  CA  HIS   102      15.760   6.779  39.430  1.00  0.00              
ATOM    167  C   HIS   102      14.293   6.757  39.849  1.00  0.00              
ATOM    168  O   HIS   102      13.418   6.468  39.026  1.00  0.00              
ATOM    169  N   SER   103      14.010   7.023  41.124  1.00  0.00              
ATOM    170  CA  SER   103      12.635   7.008  41.607  1.00  0.00              
ATOM    171  C   SER   103      11.941   8.271  41.145  1.00  0.00              
ATOM    172  O   SER   103      12.458   9.374  41.297  1.00  0.00              
ATOM    173  N   LEU   104      10.765   8.109  40.557  1.00  0.00              
ATOM    174  CA  LEU   104      10.048   9.255  40.003  1.00  0.00              
ATOM    175  C   LEU   104       8.630   9.445  40.536  1.00  0.00              
ATOM    176  O   LEU   104       8.039   8.548  41.130  1.00  0.00              
ATOM    177  N   THR   107      18.906   8.345  25.503  1.00  0.00              
ATOM    178  CA  THR   107      17.588   7.815  25.114  1.00  0.00              
ATOM    179  C   THR   107      16.474   8.340  26.022  1.00  0.00              
ATOM    180  O   THR   107      15.307   8.411  25.603  1.00  0.00              
ATOM    181  N   CYS   108      16.820   8.697  27.263  1.00  0.00              
ATOM    182  CA  CYS   108      15.838   9.221  28.206  1.00  0.00              
ATOM    183  C   CYS   108      15.182  10.502  27.698  1.00  0.00              
ATOM    184  O   CYS   108      14.032  10.794  28.036  1.00  0.00              
ATOM    185  N   LEU   109      15.929  11.265  26.903  1.00  0.00              
ATOM    186  CA  LEU   109      15.448  12.502  26.303  1.00  0.00              
ATOM    187  C   LEU   109      14.202  12.257  25.427  1.00  0.00              
ATOM    188  O   LEU   109      13.256  13.040  25.469  1.00  0.00              
ATOM    189  N   GLU   110      14.184  11.159  24.672  1.00  0.00              
ATOM    190  CA  GLU   110      13.032  10.835  23.805  1.00  0.00              
ATOM    191  C   GLU   110      11.738  10.509  24.548  1.00  0.00              
ATOM    192  O   GLU   110      10.639  10.634  23.988  1.00  0.00              
END
