REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0052AL009_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0052  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0052 Cyanovirin-N, Nostoc ellipsosporum  
METHOD This prediction is based, in part, on a threading algorithm described in   
METHOD three publications:  
METHOD (i) "A polynomial-time algorithm for a class of protein threading  
METHOD problems", by Ying Xu and Edward C. Uberbacher, CABIOS (journal)   
METHOD Vol.12, No.6, 1996 pp.511-517  
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) "An Efficient Computational Method for Globally Optimal Threading",  
METHOD by Y. Xu, D. Xu, and E.C. Uberbacher, invited paper to appear in  
METHOD Journal of Computational Biology, 1998.  
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 to  
METHOD Protein Science.  
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    
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 3hla_B 
ATOM      1  N   SER     5       0.449  39.441  65.328  1.00  0.00              
ATOM      2  CA  SER     5       0.152  40.746  64.755  1.00  0.00              
ATOM      3  C   SER     5       1.502  41.331  64.306  1.00  0.00              
ATOM      4  O   SER     5       2.448  41.277  65.077  1.00  0.00              
ATOM      5  N   GLN     6       1.633  41.920  63.110  1.00  0.00              
ATOM      6  CA  GLN     6       2.860  42.396  62.501  1.00  0.00              
ATOM      7  C   GLN     6       2.843  43.886  62.089  1.00  0.00              
ATOM      8  O   GLN     6       1.908  44.350  61.408  1.00  0.00              
ATOM      9  N   THR     7       3.916  44.634  62.383  1.00  0.00              
ATOM     10  CA  THR     7       4.073  46.002  61.894  1.00  0.00              
ATOM     11  C   THR     7       5.462  46.195  61.287  1.00  0.00              
ATOM     12  O   THR     7       6.459  45.807  61.911  1.00  0.00              
ATOM     13  N   CYS     8       5.586  46.773  60.082  1.00  0.00              
ATOM     14  CA  CYS     8       6.895  46.965  59.438  1.00  0.00              
ATOM     15  C   CYS     8       7.089  48.469  59.413  1.00  0.00              
ATOM     16  O   CYS     8       6.183  49.148  58.914  1.00  0.00              
ATOM     17  N   TYR     9       8.199  49.012  59.916  1.00  0.00              
ATOM     18  CA  TYR     9       8.403  50.474  59.981  1.00  0.00              
ATOM     19  C   TYR     9       9.868  50.918  60.079  1.00  0.00              
ATOM     20  O   TYR     9      10.709  50.077  60.294  1.00  0.00              
ATOM     21  N   ASN    10      10.177  52.226  59.985  1.00  0.00              
ATOM     22  CA  ASN    10      11.524  52.817  60.113  1.00  0.00              
ATOM     23  C   ASN    10      11.669  53.422  61.500  1.00  0.00              
ATOM     24  O   ASN    10      10.662  53.981  61.973  1.00  0.00              
ATOM     25  N   LEU    18      19.142  54.204  58.015  1.00  0.00              
ATOM     26  CA  LEU    18      17.943  54.188  58.860  1.00  0.00              
ATOM     27  C   LEU    18      17.827  52.755  59.408  1.00  0.00              
ATOM     28  O   LEU    18      18.812  52.000  59.257  1.00  0.00              
ATOM     29  N   THR    19      16.712  52.363  60.070  1.00  0.00              
ATOM     30  CA  THR    19      16.564  50.989  60.533  1.00  0.00              
ATOM     31  C   THR    19      15.189  50.473  60.183  1.00  0.00              
ATOM     32  O   THR    19      14.219  51.241  60.121  1.00  0.00              
ATOM     33  N   SER    20      15.088  49.180  59.904  1.00  0.00              
ATOM     34  CA  SER    20      13.819  48.605  59.475  1.00  0.00              
ATOM     35  C   SER    20      13.433  47.580  60.511  1.00  0.00              
ATOM     36  O   SER    20      14.171  46.629  60.758  1.00  0.00              
ATOM     37  N   THR    21      12.308  47.836  61.134  1.00  0.00              
ATOM     38  CA  THR    21      11.836  47.065  62.235  1.00  0.00              
ATOM     39  C   THR    21      10.665  46.248  61.731  1.00  0.00              
ATOM     40  O   THR    21       9.887  46.761  60.895  1.00  0.00              
ATOM     41  N   CYS    22      10.595  44.972  62.159  1.00  0.00              
ATOM     42  CA  CYS    22       9.420  44.141  61.998  1.00  0.00              
ATOM     43  C   CYS    22       9.126  43.698  63.414  1.00  0.00              
ATOM     44  O   CYS    22       9.893  42.977  64.065  1.00  0.00              
ATOM     45  N   GLU    23       8.064  44.293  63.966  1.00  0.00              
ATOM     46  CA  GLU    23       7.584  44.011  65.320  1.00  0.00              
ATOM     47  C   GLU    23       6.533  42.935  65.182  1.00  0.00              
ATOM     48  O   GLU    23       5.555  43.164  64.468  1.00  0.00              
ATOM     49  N   ARG    24       6.708  41.747  65.689  1.00  0.00              
ATOM     50  CA  ARG    24       5.653  40.792  65.579  1.00  0.00              
ATOM     51  C   ARG    24       5.267  40.610  67.030  1.00  0.00              
ATOM     52  O   ARG    24       6.148  40.507  67.901  1.00  0.00              
ATOM     53  N   THR    25       3.948  40.645  67.293  1.00  0.00              
ATOM     54  CA  THR    25       3.380  40.581  68.623  1.00  0.00              
ATOM     55  C   THR    25       2.136  39.681  68.710  1.00  0.00              
ATOM     56  O   THR    25       1.730  39.072  67.735  1.00  0.00              
ATOM     57  N   ASN    26       1.521  39.569  69.879  1.00  0.00              
ATOM     58  CA  ASN    26       0.285  38.856  70.066  1.00  0.00              
ATOM     59  C   ASN    26       0.240  37.365  69.701  1.00  0.00              
ATOM     60  O   ASN    26      -0.873  36.849  69.501  1.00  0.00              
ATOM     61  N   GLY    27       1.382  36.668  69.627  1.00  0.00              
ATOM     62  CA  GLY    27       1.361  35.274  69.279  1.00  0.00              
ATOM     63  C   GLY    27       1.724  34.282  70.403  1.00  0.00              
ATOM     64  O   GLY    27       2.179  34.558  71.529  1.00  0.00              
ATOM     65  N   ASN    30       8.277  31.044  65.753  1.00  0.00              
ATOM     66  CA  ASN    30       7.753  31.872  64.665  1.00  0.00              
ATOM     67  C   ASN    30       8.963  32.099  63.802  1.00  0.00              
ATOM     68  O   ASN    30      10.073  32.130  64.369  1.00  0.00              
ATOM     69  N   THR    31       8.843  32.171  62.489  1.00  0.00              
ATOM     70  CA  THR    31       9.977  32.526  61.658  1.00  0.00              
ATOM     71  C   THR    31       9.660  33.826  60.997  1.00  0.00              
ATOM     72  O   THR    31       8.607  34.002  60.375  1.00  0.00              
ATOM     73  N   SER    32      10.520  34.790  61.260  1.00  0.00              
ATOM     74  CA  SER    32      10.405  36.131  60.737  1.00  0.00              
ATOM     75  C   SER    32      11.688  36.381  59.988  1.00  0.00              
ATOM     76  O   SER    32      12.765  36.067  60.526  1.00  0.00              
ATOM     77  N   SER    33      11.603  36.899  58.765  1.00  0.00              
ATOM     78  CA  SER    33      12.790  37.392  58.112  1.00  0.00              
ATOM     79  C   SER    33      12.405  38.484  57.163  1.00  0.00              
ATOM     80  O   SER    33      11.292  38.516  56.641  1.00  0.00              
ATOM     81  N   ILE    34      13.241  39.542  57.218  1.00  0.00              
ATOM     82  CA  ILE    34      13.076  40.738  56.410  1.00  0.00              
ATOM     83  C   ILE    34      13.487  40.509  54.962  1.00  0.00              
ATOM     84  O   ILE    34      14.584  40.042  54.699  1.00  0.00              
ATOM     85  N   ASP    35      12.669  40.794  53.974  1.00  0.00              
ATOM     86  CA  ASP    35      13.091  40.548  52.596  1.00  0.00              
ATOM     87  C   ASP    35      13.219  41.885  51.868  1.00  0.00              
ATOM     88  O   ASP    35      12.278  42.690  51.914  1.00  0.00              
ATOM     89  N   ASN    37      14.445  39.111  47.987  1.00  0.00              
ATOM     90  CA  ASN    37      15.585  38.390  48.503  1.00  0.00              
ATOM     91  C   ASN    37      15.584  38.556  50.017  1.00  0.00              
ATOM     92  O   ASN    37      15.161  39.566  50.565  1.00  0.00              
ATOM     93  N   SER    38      15.940  37.537  50.760  1.00  0.00              
ATOM     94  CA  SER    38      15.936  37.614  52.216  1.00  0.00              
ATOM     95  C   SER    38      17.172  38.330  52.616  1.00  0.00              
ATOM     96  O   SER    38      18.186  38.081  51.995  1.00  0.00              
ATOM     97  N   GLU    41      19.204  41.606  63.047  1.00  0.00              
ATOM     98  CA  GLU    41      19.245  41.312  64.469  1.00  0.00              
ATOM     99  C   GLU    41      17.817  41.165  65.026  1.00  0.00              
ATOM    100  O   GLU    41      16.843  41.279  64.281  1.00  0.00              
ATOM    101  N   ASN    42      17.586  40.874  66.315  1.00  0.00              
ATOM    102  CA  ASN    42      16.235  40.773  66.886  1.00  0.00              
ATOM    103  C   ASN    42      16.346  40.777  68.402  1.00  0.00              
ATOM    104  O   ASN    42      17.372  40.361  68.934  1.00  0.00              
ATOM    105  N   ASP    44      10.273  37.950  74.928  1.00  0.00              
ATOM    106  CA  ASP    44       9.488  38.301  76.040  1.00  0.00              
ATOM    107  C   ASP    44       8.009  38.228  75.599  1.00  0.00              
ATOM    108  O   ASP    44       7.662  38.032  74.408  1.00  0.00              
ATOM    109  N   GLY    45       7.163  38.427  76.621  1.00  0.00              
ATOM    110  CA  GLY    45       5.734  38.289  76.585  1.00  0.00              
ATOM    111  C   GLY    45       5.088  39.393  77.358  1.00  0.00              
ATOM    112  O   GLY    45       5.672  39.939  78.310  1.00  0.00              
ATOM    113  N   SER    46       6.163  38.632  71.849  1.00  0.00              
ATOM    114  CA  SER    46       6.459  39.690  70.858  1.00  0.00              
ATOM    115  C   SER    46       7.970  39.751  70.761  1.00  0.00              
ATOM    116  O   SER    46       8.594  39.494  71.795  1.00  0.00              
ATOM    117  N   LEU    47       8.458  40.185  69.591  1.00  0.00              
ATOM    118  CA  LEU    47       9.839  40.197  69.109  1.00  0.00              
ATOM    119  C   LEU    47      10.025  41.370  68.142  1.00  0.00              
ATOM    120  O   LEU    47       9.132  41.677  67.377  1.00  0.00              
ATOM    121  N   LYS    48      11.152  42.076  68.142  1.00  0.00              
ATOM    122  CA  LYS    48      11.440  43.064  67.124  1.00  0.00              
ATOM    123  C   LYS    48      12.640  42.560  66.319  1.00  0.00              
ATOM    124  O   LYS    48      13.646  42.175  66.925  1.00  0.00              
ATOM    125  N   TRP    49      12.524  42.453  65.001  1.00  0.00              
ATOM    126  CA  TRP    49      13.626  42.089  64.118  1.00  0.00              
ATOM    127  C   TRP    49      14.046  43.338  63.400  1.00  0.00              
ATOM    128  O   TRP    49      13.173  44.151  63.039  1.00  0.00              
ATOM    129  N   GLN    50      15.347  43.554  63.190  1.00  0.00              
ATOM    130  CA  GLN    50      15.715  44.780  62.519  1.00  0.00              
ATOM    131  C   GLN    50      16.986  44.668  61.747  1.00  0.00              
ATOM    132  O   GLN    50      17.782  43.776  62.001  1.00  0.00              
ATOM    133  N   PRO    51      17.138  45.607  60.823  1.00  0.00              
ATOM    134  CA  PRO    51      18.286  45.670  59.963  1.00  0.00              
ATOM    135  C   PRO    51      18.501  47.167  59.703  1.00  0.00              
ATOM    136  O   PRO    51      17.553  47.979  59.799  1.00  0.00              
ATOM    137  N   SER    52      19.763  47.554  59.503  1.00  0.00              
ATOM    138  CA  SER    52      20.097  48.879  59.066  1.00  0.00              
ATOM    139  C   SER    52      19.882  48.908  57.570  1.00  0.00              
ATOM    140  O   SER    52      20.203  47.950  56.879  1.00  0.00              
ATOM    141  N   GLU    56      10.865  46.898  50.466  1.00  0.00              
ATOM    142  CA  GLU    56      11.199  46.046  51.631  1.00  0.00              
ATOM    143  C   GLU    56       9.934  45.408  52.156  1.00  0.00              
ATOM    144  O   GLU    56       8.824  45.857  51.856  1.00  0.00              
ATOM    145  N   THR    57      10.066  44.321  52.895  1.00  0.00              
ATOM    146  CA  THR    57       8.933  43.567  53.415  1.00  0.00              
ATOM    147  C   THR    57       9.420  42.740  54.570  1.00  0.00              
ATOM    148  O   THR    57      10.619  42.583  54.789  1.00  0.00              
ATOM    149  N   CYS    58       8.496  42.191  55.316  1.00  0.00              
ATOM    150  CA  CYS    58       8.795  41.325  56.433  1.00  0.00              
ATOM    151  C   CYS    58       7.921  40.103  56.174  1.00  0.00              
ATOM    152  O   CYS    58       6.745  40.271  55.829  1.00  0.00              
ATOM    153  N   ARG    59       8.482  38.892  56.179  1.00  0.00              
ATOM    154  CA  ARG    59       7.759  37.663  55.920  1.00  0.00              
ATOM    155  C   ARG    59       7.683  37.004  57.283  1.00  0.00              
ATOM    156  O   ARG    59       8.695  36.977  58.005  1.00  0.00              
ATOM    157  N   ASN    60       6.501  36.514  57.676  1.00  0.00              
ATOM    158  CA  ASN    60       6.322  35.821  58.954  1.00  0.00              
ATOM    159  C   ASN    60       5.544  34.508  58.752  1.00  0.00              
ATOM    160  O   ASN    60       4.624  34.336  57.952  1.00  0.00              
ATOM    161  N   THR    61       5.940  33.490  59.457  1.00  0.00              
ATOM    162  CA  THR    61       5.365  32.202  59.277  1.00  0.00              
ATOM    163  C   THR    61       5.280  31.643  60.676  1.00  0.00              
ATOM    164  O   THR    61       6.282  31.734  61.394  1.00  0.00              
ATOM    165  N   ASN    62       4.113  31.145  61.117  1.00  0.00              
ATOM    166  CA  ASN    62       3.894  30.691  62.476  1.00  0.00              
ATOM    167  C   ASN    62       2.926  29.533  62.423  1.00  0.00              
ATOM    168  O   ASN    62       2.188  29.425  61.445  1.00  0.00              
ATOM    169  N   ALA    71       2.987  35.281  56.102  1.00  0.00              
ATOM    170  CA  ALA    71       2.465  36.609  55.789  1.00  0.00              
ATOM    171  C   ALA    71       3.563  37.594  55.483  1.00  0.00              
ATOM    172  O   ALA    71       4.405  37.869  56.332  1.00  0.00              
ATOM    173  N   GLU    72       3.556  38.101  54.261  1.00  0.00              
ATOM    174  CA  GLU    72       4.517  39.073  53.783  1.00  0.00              
ATOM    175  C   GLU    72       3.932  40.471  53.909  1.00  0.00              
ATOM    176  O   GLU    72       3.134  40.848  53.047  1.00  0.00              
ATOM    177  N   CYS    73       4.216  41.237  54.963  1.00  0.00              
ATOM    178  CA  CYS    73       3.720  42.609  54.975  1.00  0.00              
ATOM    179  C   CYS    73       4.827  43.579  54.588  1.00  0.00              
ATOM    180  O   CYS    73       5.908  43.623  55.165  1.00  0.00              
ATOM    181  N   LYS    74       4.564  44.259  53.481  1.00  0.00              
ATOM    182  CA  LYS    74       5.451  45.247  52.863  1.00  0.00              
ATOM    183  C   LYS    74       5.598  46.561  53.655  1.00  0.00              
ATOM    184  O   LYS    74       4.694  46.946  54.387  1.00  0.00              
END
