REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0052AL009_3 
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 3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2mcm 
ATOM      1  N   LYS     3      21.507  24.135   9.096  1.00  0.00              
ATOM      2  CA  LYS     3      20.423  23.488   9.823  1.00  0.00              
ATOM      3  C   LYS     3      19.859  22.380   8.950  1.00  0.00              
ATOM      4  O   LYS     3      19.493  22.671   7.787  1.00  0.00              
ATOM      5  N   PHE     4      19.778  21.161   9.471  1.00  0.00              
ATOM      6  CA  PHE     4      19.158  20.041   8.784  1.00  0.00              
ATOM      7  C   PHE     4      17.871  19.636   9.486  1.00  0.00              
ATOM      8  O   PHE     4      17.836  19.625  10.765  1.00  0.00              
ATOM      9  N   SER     5      16.823  19.369   8.792  1.00  0.00              
ATOM     10  CA  SER     5      15.531  18.911   9.287  1.00  0.00              
ATOM     11  C   SER     5      15.573  17.400   9.317  1.00  0.00              
ATOM     12  O   SER     5      15.731  16.750   8.274  1.00  0.00              
ATOM     13  N   GLN     6      15.466  16.793  10.484  1.00  0.00              
ATOM     14  CA  GLN     6      15.497  15.328  10.712  1.00  0.00              
ATOM     15  C   GLN     6      14.123  14.795  10.765  1.00  0.00              
ATOM     16  O   GLN     6      13.217  15.417  11.493  1.00  0.00              
ATOM     17  N   THR     7      13.694  13.772  10.041  1.00  0.00              
ATOM     18  CA  THR     7      12.286  13.342  10.146  1.00  0.00              
ATOM     19  C   THR     7      12.038  11.988   9.512  1.00  0.00              
ATOM     20  O   THR     7      12.933  11.408   8.856  1.00  0.00              
ATOM     21  N   CYS     8      10.845  11.490   9.722  1.00  0.00              
ATOM     22  CA  CYS     8      10.374  10.214   9.137  1.00  0.00              
ATOM     23  C   CYS     8       9.434  10.623   8.019  1.00  0.00              
ATOM     24  O   CYS     8       8.510  11.433   8.139  1.00  0.00              
ATOM     25  N   TYR     9       9.694  10.083   6.804  1.00  0.00              
ATOM     26  CA  TYR     9       8.934  10.477   5.608  1.00  0.00              
ATOM     27  C   TYR     9       8.611   9.297   4.685  1.00  0.00              
ATOM     28  O   TYR     9       9.144   8.213   4.906  1.00  0.00              
ATOM     29  N   ASN    10       7.829   9.574   3.665  1.00  0.00              
ATOM     30  CA  ASN    10       7.473   8.544   2.678  1.00  0.00              
ATOM     31  C   ASN    10       7.055   9.333   1.440  1.00  0.00              
ATOM     32  O   ASN    10       6.775  10.491   1.508  1.00  0.00              
ATOM     33  N   SER    11       7.034   8.590   0.315  1.00  0.00              
ATOM     34  CA  SER    11       6.550   9.226  -0.945  1.00  0.00              
ATOM     35  C   SER    11       5.034   8.999  -0.926  1.00  0.00              
ATOM     36  O   SER    11       4.539   7.840  -0.941  1.00  0.00              
ATOM     37  N   ALA    12       4.317  10.125  -0.851  1.00  0.00              
ATOM     38  CA  ALA    12       2.841   9.980  -0.773  1.00  0.00              
ATOM     39  C   ALA    12       2.274   9.933  -2.183  1.00  0.00              
ATOM     40  O   ALA    12       1.303   9.226  -2.449  1.00  0.00              
ATOM     41  N   ILE    13       2.922  10.698  -3.034  1.00  0.00              
ATOM     42  CA  ILE    13       2.581  10.779  -4.448  1.00  0.00              
ATOM     43  C   ILE    13       3.864  11.078  -5.195  1.00  0.00              
ATOM     44  O   ILE    13       4.744  11.867  -4.775  1.00  0.00              
ATOM     45  N   THR    19       6.149  13.782  -4.629  1.00  0.00              
ATOM     46  CA  THR    19       5.736  14.461  -3.383  1.00  0.00              
ATOM     47  C   THR    19       6.037  13.573  -2.138  1.00  0.00              
ATOM     48  O   THR    19       5.482  12.507  -1.969  1.00  0.00              
ATOM     49  N   SER    20       6.899  14.145  -1.354  1.00  0.00              
ATOM     50  CA  SER    20       7.328  13.519  -0.071  1.00  0.00              
ATOM     51  C   SER    20       6.494  14.152   1.065  1.00  0.00              
ATOM     52  O   SER    20       6.283  15.360   1.088  1.00  0.00              
ATOM     53  N   THR    21       6.006  13.242   1.932  1.00  0.00              
ATOM     54  CA  THR    21       5.245  13.768   3.109  1.00  0.00              
ATOM     55  C   THR    21       5.991  13.296   4.362  1.00  0.00              
ATOM     56  O   THR    21       6.500  12.155   4.355  1.00  0.00              
ATOM     57  N   CYS    22       6.065  14.035   5.450  1.00  0.00              
ATOM     58  CA  CYS    22       6.802  13.626   6.654  1.00  0.00              
ATOM     59  C   CYS    22       5.920  13.871   7.922  1.00  0.00              
ATOM     60  O   CYS    22       4.953  14.628   7.824  1.00  0.00              
ATOM     61  N   GLU    23       6.335  13.310   9.010  1.00  0.00              
ATOM     62  CA  GLU    23       5.635  13.466  10.334  1.00  0.00              
ATOM     63  C   GLU    23       6.186  14.753  10.941  1.00  0.00              
ATOM     64  O   GLU    23       7.295  14.788  11.421  1.00  0.00              
ATOM     65  N   SER    32      12.621  17.244  13.901  1.00  0.00              
ATOM     66  CA  SER    32      13.379  18.168  14.718  1.00  0.00              
ATOM     67  C   SER    32      14.448  18.847  13.889  1.00  0.00              
ATOM     68  O   SER    32      14.802  18.236  12.828  1.00  0.00              
ATOM     69  N   SER    33      15.006  19.931  14.283  1.00  0.00              
ATOM     70  CA  SER    33      16.088  20.631  13.529  1.00  0.00              
ATOM     71  C   SER    33      17.362  20.524  14.276  1.00  0.00              
ATOM     72  O   SER    33      17.376  20.816  15.528  1.00  0.00              
ATOM     73  N   ILE    34      18.502  20.205  13.653  1.00  0.00              
ATOM     74  CA  ILE    34      19.779  20.155  14.279  1.00  0.00              
ATOM     75  C   ILE    34      20.817  20.866  13.398  1.00  0.00              
ATOM     76  O   ILE    34      20.659  20.681  12.160  1.00  0.00              
ATOM     77  N   ASP    35      21.664  21.647  13.923  1.00  0.00              
ATOM     78  CA  ASP    35      22.745  22.319  13.135  1.00  0.00              
ATOM     79  C   ASP    35      23.934  21.452  13.143  1.00  0.00              
ATOM     80  O   ASP    35      24.477  20.898  14.137  1.00  0.00              
ATOM     81  N   VAL    43      26.054  15.232  12.603  1.00  0.00              
ATOM     82  CA  VAL    43      24.842  15.357  13.394  1.00  0.00              
ATOM     83  C   VAL    43      24.559  13.949  13.953  1.00  0.00              
ATOM     84  O   VAL    43      24.649  12.937  13.225  1.00  0.00              
ATOM     85  N   ASP    44      24.197  13.928  15.255  1.00  0.00              
ATOM     86  CA  ASP    44      23.762  12.620  15.836  1.00  0.00              
ATOM     87  C   ASP    44      22.444  13.018  16.545  1.00  0.00              
ATOM     88  O   ASP    44      22.585  13.907  17.430  1.00  0.00              
ATOM     89  N   GLY    45      21.344  12.453  16.140  1.00  0.00              
ATOM     90  CA  GLY    45      20.067  12.812  16.740  1.00  0.00              
ATOM     91  C   GLY    45      19.170  11.618  16.980  1.00  0.00              
ATOM     92  O   GLY    45      19.163  10.634  16.249  1.00  0.00              
ATOM     93  N   SER    46      18.343  11.771  18.008  1.00  0.00              
ATOM     94  CA  SER    46      17.326  10.762  18.338  1.00  0.00              
ATOM     95  C   SER    46      16.060  11.145  17.621  1.00  0.00              
ATOM     96  O   SER    46      15.680  12.357  17.659  1.00  0.00              
ATOM     97  N   LEU    47      15.341  10.211  17.089  1.00  0.00              
ATOM     98  CA  LEU    47      14.101  10.406  16.399  1.00  0.00              
ATOM     99  C   LEU    47      13.093   9.329  16.819  1.00  0.00              
ATOM    100  O   LEU    47      13.473   8.160  16.740  1.00  0.00              
ATOM    101  N   LYS    48      11.896   9.749  17.228  1.00  0.00              
ATOM    102  CA  LYS    48      10.894   8.711  17.573  1.00  0.00              
ATOM    103  C   LYS    48      10.138   8.341  16.312  1.00  0.00              
ATOM    104  O   LYS    48       9.565   9.294  15.664  1.00  0.00              
ATOM    105  N   TRP    49      10.041   7.090  15.937  1.00  0.00              
ATOM    106  CA  TRP    49       9.325   6.703  14.703  1.00  0.00              
ATOM    107  C   TRP    49       8.042   5.974  15.015  1.00  0.00              
ATOM    108  O   TRP    49       7.875   5.377  16.106  1.00  0.00              
ATOM    109  N   THR    57       2.585   4.187  11.658  1.00  0.00              
ATOM    110  CA  THR    57       1.622   4.937  10.825  1.00  0.00              
ATOM    111  C   THR    57       1.762   6.379  11.309  1.00  0.00              
ATOM    112  O   THR    57       1.976   6.593  12.554  1.00  0.00              
ATOM    113  N   CYS    58       1.625   7.339  10.442  1.00  0.00              
ATOM    114  CA  CYS    58       1.721   8.764  10.885  1.00  0.00              
ATOM    115  C   CYS    58       0.888   9.606   9.951  1.00  0.00              
ATOM    116  O   CYS    58       0.501   9.155   8.871  1.00  0.00              
ATOM    117  N   ARG    59       0.574  10.833  10.371  1.00  0.00              
ATOM    118  CA  ARG    59      -0.144  11.803   9.553  1.00  0.00              
ATOM    119  C   ARG    59       0.975  12.602   8.856  1.00  0.00              
ATOM    120  O   ARG    59       1.848  13.203   9.490  1.00  0.00              
ATOM    121  N   ASN    60       0.934  12.507   7.532  1.00  0.00              
ATOM    122  CA  ASN    60       1.996  13.196   6.767  1.00  0.00              
ATOM    123  C   ASN    60       1.579  14.628   6.421  1.00  0.00              
ATOM    124  O   ASN    60       0.373  14.838   6.193  1.00  0.00              
ATOM    125  N   THR    61       2.581  15.513   6.440  1.00  0.00              
ATOM    126  CA  THR    61       2.352  16.906   5.990  1.00  0.00              
ATOM    127  C   THR    61       3.254  17.070   4.711  1.00  0.00              
ATOM    128  O   THR    61       4.289  16.356   4.685  1.00  0.00              
ATOM    129  N   ASN    62       2.758  17.866   3.781  1.00  0.00              
ATOM    130  CA  ASN    62       3.548  18.090   2.521  1.00  0.00              
ATOM    131  C   ASN    62       3.809  19.558   2.284  1.00  0.00              
ATOM    132  O   ASN    62       3.049  20.443   2.723  1.00  0.00              
ATOM    133  N   ALA    64       1.122  21.388   5.022  1.00  0.00              
ATOM    134  CA  ALA    64      -0.292  21.089   4.779  1.00  0.00              
ATOM    135  C   ALA    64      -0.525  19.615   5.060  1.00  0.00              
ATOM    136  O   ALA    64       0.157  18.733   4.482  1.00  0.00              
ATOM    137  N   GLY    65      -1.545  19.266   5.836  1.00  0.00              
ATOM    138  CA  GLY    65      -1.883  17.866   6.095  1.00  0.00              
ATOM    139  C   GLY    65      -2.320  17.173   4.820  1.00  0.00              
ATOM    140  O   GLY    65      -3.103  17.653   3.976  1.00  0.00              
ATOM    141  N   SER    66      -1.773  15.975   4.651  1.00  0.00              
ATOM    142  CA  SER    66      -2.110  15.126   3.511  1.00  0.00              
ATOM    143  C   SER    66      -2.963  13.949   3.920  1.00  0.00              
ATOM    144  O   SER    66      -3.973  13.626   3.263  1.00  0.00              
ATOM    145  N   SER    67      -2.610  13.285   4.989  1.00  0.00              
ATOM    146  CA  SER    67      -3.420  12.073   5.337  1.00  0.00              
ATOM    147  C   SER    67      -2.494  11.046   5.956  1.00  0.00              
ATOM    148  O   SER    67      -1.314  11.305   6.294  1.00  0.00              
ATOM    149  N   GLU    68      -3.056   9.862   6.211  1.00  0.00              
ATOM    150  CA  GLU    68      -2.332   8.839   6.905  1.00  0.00              
ATOM    151  C   GLU    68      -1.390   8.064   6.016  1.00  0.00              
ATOM    152  O   GLU    68      -1.823   7.723   4.884  1.00  0.00              
ATOM    153  N   LEU    69      -0.240   7.744   6.511  1.00  0.00              
ATOM    154  CA  LEU    69       0.763   6.920   5.859  1.00  0.00              
ATOM    155  C   LEU    69       0.976   5.686   6.767  1.00  0.00              
ATOM    156  O   LEU    69       1.285   5.843   7.944  1.00  0.00              
ATOM    157  N   ALA    70       0.881   4.485   6.215  1.00  0.00              
ATOM    158  CA  ALA    70       1.096   3.255   7.003  1.00  0.00              
ATOM    159  C   ALA    70       2.410   2.666   6.508  1.00  0.00              
ATOM    160  O   ALA    70       2.444   2.253   5.296  1.00  0.00              
ATOM    161  N   CYS    73       8.871   3.654   4.156  1.00  0.00              
ATOM    162  CA  CYS    73       9.150   4.940   4.827  1.00  0.00              
ATOM    163  C   CYS    73      10.626   5.061   5.109  1.00  0.00              
ATOM    164  O   CYS    73      11.345   3.984   5.022  1.00  0.00              
ATOM    165  N   LYS    74      11.141   6.216   5.390  1.00  0.00              
ATOM    166  CA  LYS    74      12.535   6.387   5.709  1.00  0.00              
ATOM    167  C   LYS    74      12.714   7.325   6.905  1.00  0.00              
ATOM    168  O   LYS    74      11.749   7.993   7.337  1.00  0.00              
ATOM    169  N   THR    75      13.883   7.360   7.442  1.00  0.00              
ATOM    170  CA  THR    75      14.337   8.327   8.451  1.00  0.00              
ATOM    171  C   THR    75      15.583   8.977   7.794  1.00  0.00              
ATOM    172  O   THR    75      16.395   8.288   7.160  1.00  0.00              
ATOM    173  N   ARG    76      15.694  10.314   7.937  1.00  0.00              
ATOM    174  CA  ARG    76      16.883  10.907   7.299  1.00  0.00              
ATOM    175  C   ARG    76      16.878  12.379   7.625  1.00  0.00              
ATOM    176  O   ARG    76      16.140  12.794   8.559  1.00  0.00              
ATOM    177  N   ALA    77      17.681  13.168   6.958  1.00  0.00              
ATOM    178  CA  ALA    77      17.787  14.596   7.187  1.00  0.00              
ATOM    179  C   ALA    77      18.080  15.371   5.908  1.00  0.00              
ATOM    180  O   ALA    77      18.653  14.767   5.004  1.00  0.00              
ATOM    181  N   GLN    78      17.591  16.608   5.878  1.00  0.00              
ATOM    182  CA  GLN    78      17.871  17.390   4.651  1.00  0.00              
ATOM    183  C   GLN    78      17.826  18.858   5.026  1.00  0.00              
ATOM    184  O   GLN    78      17.116  19.266   5.960  1.00  0.00              
ATOM    185  N   ASN    86      21.283  16.256   1.767  1.00  0.00              
ATOM    186  CA  ASN    86      21.034  15.353   2.922  1.00  0.00              
ATOM    187  C   ASN    86      21.049  13.914   2.464  1.00  0.00              
ATOM    188  O   ASN    86      21.609  13.569   1.407  1.00  0.00              
ATOM    189  N   LEU    87      20.448  13.054   3.293  1.00  0.00              
ATOM    190  CA  LEU    87      20.425  11.618   2.937  1.00  0.00              
ATOM    191  C   LEU    87      19.325  10.950   3.758  1.00  0.00              
ATOM    192  O   LEU    87      18.870  11.575   4.775  1.00  0.00              
ATOM    193  N   ASP    88      18.918   9.777   3.413  1.00  0.00              
ATOM    194  CA  ASP    88      17.870   9.063   4.118  1.00  0.00              
ATOM    195  C   ASP    88      18.138   7.570   4.013  1.00  0.00              
ATOM    196  O   ASP    88      18.864   7.058   3.136  1.00  0.00              
ATOM    197  N   ASP    89      17.589   6.809   4.966  1.00  0.00              
ATOM    198  CA  ASP    89      17.710   5.359   4.977  1.00  0.00              
ATOM    199  C   ASP    89      16.360   4.702   5.090  1.00  0.00              
ATOM    200  O   ASP    89      15.561   5.128   6.035  1.00  0.00              
ATOM    201  N   HIS    90      15.910   3.789   4.295  1.00  0.00              
ATOM    202  CA  HIS    90      14.604   3.110   4.373  1.00  0.00              
ATOM    203  C   HIS    90      14.614   2.278   5.713  1.00  0.00              
ATOM    204  O   HIS    90      15.649   1.770   6.118  1.00  0.00              
ATOM    205  N   ILE    91      13.410   2.331   6.331  1.00  0.00              
ATOM    206  CA  ILE    91      13.342   1.567   7.633  1.00  0.00              
ATOM    207  C   ILE    91      12.150   0.636   7.472  1.00  0.00              
ATOM    208  O   ILE    91      11.245   0.817   6.643  1.00  0.00              
END
