REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL201_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : TATSUYA-AKUTSU 
REMARK  ---------------------------------------------------------- 
TARGET T0065  
AUTHOR 7648-2940-6918  
REMARK   
METHOD We align a target sequence with structurally aligned sequences  
METHOD (i.e., multiple structure alignment), where a multiple structure  
METHOD alignment is computed from results of pairwise structure alignments  
METHOD for similar structures.   
METHOD Pairwise structure alignments are computed using a computer  
METHOD program STRALIGN [1] developed by the group-leader and they are  
METHOD combined into a multiple structure alignment using a method like  
METHOD center-star alignment.  
METHOD A simple dynamic programming procedure (Smith-Waterman like procedure)  
METHOD is used for computing an alignment between a target sequence and  
METHOD the aligned sequences.  
METHOD Finally, an alignment between a target and one of the aligned  
METHOD sequences (i.e., template sequence) is extracted and refined.  
METHOD Human knowledge is also used to find template structures and  
METHOD to refine alignments.  
METHOD  
METHOD [1] T. Akutsu: Protein structure alignment using dynamic programming  
METHOD and iterative alignment, IEICE Transactions on Information and Systems,  
METHOD vol. E79-D, pp. 1629--1636, 1996.  
METHOD  
METHOD Program code of STRALIGN is available via  
METHOD http://www.hgc.ims.u-tokyo.ac.jp/service/tooldoc/stralign/intro.html  
MODEL  1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1add 
ATOM      1  N   ASP B  12     -11.036  40.598  23.958  1.00  0.00              
ATOM      2  CA  ASP B  12      -9.687  40.964  23.579  1.00  0.00              
ATOM      3  C   ASP B  12      -9.078  42.000  24.526  1.00  0.00              
ATOM      4  O   ASP B  12      -7.856  42.122  24.600  1.00  0.00              
ATOM      5  N   GLN B  13      -9.875  42.899  25.129  1.00  0.00              
ATOM      6  CA  GLN B  13      -9.264  43.858  26.038  1.00  0.00              
ATOM      7  C   GLN B  13      -8.660  43.112  27.199  1.00  0.00              
ATOM      8  O   GLN B  13      -7.790  43.645  27.875  1.00  0.00              
ATOM      9  N   GLU B  14      -9.404  42.129  27.703  1.00  0.00              
ATOM     10  CA  GLU B  14      -8.919  41.351  28.821  1.00  0.00              
ATOM     11  C   GLU B  14      -7.680  40.563  28.435  1.00  0.00              
ATOM     12  O   GLU B  14      -6.672  40.640  29.126  1.00  0.00              
ATOM     13  N   TRP B  15      -7.569  40.160  27.175  1.00  0.00              
ATOM     14  CA  TRP B  15      -6.388  39.417  26.773  1.00  0.00              
ATOM     15  C   TRP B  15      -5.156  40.317  26.754  1.00  0.00              
ATOM     16  O   TRP B  15      -4.081  39.939  27.223  1.00  0.00              
ATOM     17  N   VAL B  16      -5.312  41.562  26.288  1.00  0.00              
ATOM     18  CA  VAL B  16      -4.195  42.494  26.237  1.00  0.00              
ATOM     19  C   VAL B  16      -3.829  42.980  27.626  1.00  0.00              
ATOM     20  O   VAL B  16      -2.666  42.955  28.014  1.00  0.00              
ATOM     21  N   GLU B  17      -4.826  43.025  28.494  1.00  0.00              
ATOM     22  CA  GLU B  17      -4.619  43.475  29.853  1.00  0.00              
ATOM     23  C   GLU B  17      -3.915  42.435  30.707  1.00  0.00              
ATOM     24  O   GLU B  17      -2.868  42.709  31.306  1.00  0.00              
ATOM     25  N   LEU B  18      -4.308  41.166  30.592  1.00  0.00              
ATOM     26  CA  LEU B  18      -3.651  40.171  31.401  1.00  0.00              
ATOM     27  C   LEU B  18      -2.246  39.876  30.899  1.00  0.00              
ATOM     28  O   LEU B  18      -1.314  39.835  31.706  1.00  0.00              
ATOM     29  N   MET B  19      -1.994  40.179  29.622  1.00  0.00              
ATOM     30  CA  MET B  19      -0.662  39.975  29.079  1.00  0.00              
ATOM     31  C   MET B  19       0.257  41.114  29.514  1.00  0.00              
ATOM     32  O   MET B  19       1.471  40.969  29.583  1.00  0.00              
ATOM     33  N   VAL B  20      -0.264  42.338  29.560  1.00  0.00              
ATOM     34  CA  VAL B  20       0.542  43.450  30.002  1.00  0.00              
ATOM     35  C   VAL B  20       0.905  43.231  31.463  1.00  0.00              
ATOM     36  O   VAL B  20       2.050  43.387  31.879  1.00  0.00              
ATOM     37  N   GLU B  21       0.002  42.634  32.236  1.00  0.00              
ATOM     38  CA  GLU B  21       0.316  42.348  33.628  1.00  0.00              
ATOM     39  C   GLU B  21       1.376  41.254  33.736  1.00  0.00              
ATOM     40  O   GLU B  21       2.099  41.138  34.729  1.00  0.00              
ATOM     41  N   ALA B  22       1.298  40.258  32.867  1.00  0.00              
ATOM     42  CA  ALA B  22       2.284  39.206  32.925  1.00  0.00              
ATOM     43  C   ALA B  22       3.654  39.761  32.596  1.00  0.00              
ATOM     44  O   ALA B  22       4.648  39.405  33.217  1.00  0.00              
ATOM     45  N   LYS B  23       3.730  40.762  31.722  1.00  0.00              
ATOM     46  CA  LYS B  23       5.025  41.331  31.395  1.00  0.00              
ATOM     47  C   LYS B  23       5.551  42.126  32.579  1.00  0.00              
ATOM     48  O   LYS B  23       6.699  41.980  32.997  1.00  0.00              
ATOM     49  N   GLU B  24       4.643  42.785  33.295  1.00  0.00              
ATOM     50  CA  GLU B  24       5.049  43.548  34.456  1.00  0.00              
ATOM     51  C   GLU B  24       5.483  42.615  35.562  1.00  0.00              
ATOM     52  O   GLU B  24       6.242  43.003  36.451  1.00  0.00              
ATOM     53  N   ALA B  25       4.777  41.485  35.677  1.00  0.00              
ATOM     54  CA  ALA B  25       5.078  40.515  36.712  1.00  0.00              
ATOM     55  C   ALA B  25       6.241  39.603  36.358  1.00  0.00              
ATOM     56  O   ALA B  25       6.519  38.667  37.093  1.00  0.00              
ATOM     57  N   ASN B  26       6.722  39.653  35.118  1.00  0.00              
ATOM     58  CA  ASN B  26       7.840  38.817  34.738  1.00  0.00              
ATOM     59  C   ASN B  26       9.035  39.061  35.642  1.00  0.00              
ATOM     60  O   ASN B  26       8.991  39.927  36.514  1.00  0.00              
ATOM     61  N   ILE B  27       9.978  38.122  35.670  1.00  0.00              
ATOM     62  CA  ILE B  27      11.149  38.276  36.509  1.00  0.00              
ATOM     63  C   ILE B  27      12.313  38.825  35.698  1.00  0.00              
ATOM     64  O   ILE B  27      13.491  38.607  35.988  1.00  0.00              
ATOM     65  N   SER B  28      12.004  39.635  34.701  1.00  0.00              
ATOM     66  CA  SER B  28      13.049  40.220  33.888  1.00  0.00              
ATOM     67  C   SER B  28      13.679  41.345  34.691  1.00  0.00              
ATOM     68  O   SER B  28      13.172  41.712  35.745  1.00  0.00              
ATOM     69  N   PRO B  29      14.889  41.780  34.371  1.00  0.00              
ATOM     70  CA  PRO B  29      15.412  42.929  35.096  1.00  0.00              
ATOM     71  C   PRO B  29      14.689  44.176  34.604  1.00  0.00              
ATOM     72  O   PRO B  29      13.949  44.092  33.635  1.00  0.00              
ATOM     73  N   GLU B  30      14.614  45.234  35.411  1.00  0.00              
ATOM     74  CA  GLU B  30      13.892  46.430  34.996  1.00  0.00              
ATOM     75  C   GLU B  30      14.068  46.817  33.540  1.00  0.00              
ATOM     76  O   GLU B  30      13.107  47.189  32.879  1.00  0.00              
ATOM     77  N   GLU B  31      15.307  47.042  33.124  1.00  0.00              
ATOM     78  CA  GLU B  31      15.585  47.448  31.756  1.00  0.00              
ATOM     79  C   GLU B  31      14.942  46.541  30.723  1.00  0.00              
ATOM     80  O   GLU B  31      14.499  47.009  29.676  1.00  0.00              
ATOM     81  N   ILE B  32      15.138  45.229  30.841  1.00  0.00              
ATOM     82  CA  ILE B  32      14.551  44.315  29.876  1.00  0.00              
ATOM     83  C   ILE B  32      13.038  44.290  29.973  1.00  0.00              
ATOM     84  O   ILE B  32      12.338  43.965  29.017  1.00  0.00              
ATOM     85  N   ARG B  33      12.527  44.423  31.185  1.00  0.00              
ATOM     86  CA  ARG B  33      11.099  44.413  31.391  1.00  0.00              
ATOM     87  C   ARG B  33      10.472  45.603  30.706  1.00  0.00              
ATOM     88  O   ARG B  33       9.472  45.472  30.007  1.00  0.00              
ATOM     89  N   LYS B  34      11.156  46.750  30.760  1.00  0.00              
ATOM     90  CA  LYS B  34      10.658  47.945  30.115  1.00  0.00              
ATOM     91  C   LYS B  34      10.563  47.693  28.626  1.00  0.00              
ATOM     92  O   LYS B  34       9.596  48.088  27.977  1.00  0.00              
ATOM     93  N   TYR B  35      11.605  47.107  28.034  1.00  0.00              
ATOM     94  CA  TYR B  35      11.566  46.819  26.611  1.00  0.00              
ATOM     95  C   TYR B  35      10.391  45.926  26.252  1.00  0.00              
ATOM     96  O   TYR B  35      10.002  45.876  25.094  1.00  0.00              
ATOM     97  N   LEU B  36      10.135  44.911  27.076  1.00  0.00              
ATOM     98  CA  LEU B  36       9.019  44.015  26.828  1.00  0.00              
ATOM     99  C   LEU B  36       7.724  44.797  26.797  1.00  0.00              
ATOM    100  O   LEU B  36       7.017  44.811  25.803  1.00  0.00              
ATOM    101  N   LEU B  37       7.564  45.718  27.740  1.00  0.00              
ATOM    102  CA  LEU B  37       6.352  46.515  27.805  1.00  0.00              
ATOM    103  C   LEU B  37       6.264  47.493  26.665  1.00  0.00              
ATOM    104  O   LEU B  37       5.261  47.531  25.960  1.00  0.00              
ATOM    105  N   LEU B  38       7.422  47.912  26.192  1.00  0.00              
ATOM    106  CA  LEU B  38       7.473  48.843  25.088  1.00  0.00              
ATOM    107  C   LEU B  38       7.022  48.149  23.817  1.00  0.00              
ATOM    108  O   LEU B  38       6.108  48.619  23.144  1.00  0.00              
ATOM    109  N   ASN B  39       7.329  46.847  23.758  1.00  0.00              
ATOM    110  CA  ASN B  39       6.985  46.007  22.624  1.00  0.00              
ATOM    111  C   ASN B  39       5.504  45.698  22.545  1.00  0.00              
ATOM    112  O   ASN B  39       4.921  45.682  21.464  1.00  0.00              
ATOM    113  N   LYS B  40       4.925  45.187  23.626  1.00  0.00              
ATOM    114  CA  LYS B  40       3.519  44.842  23.578  1.00  0.00              
ATOM    115  C   LYS B  40       2.626  46.027  23.259  1.00  0.00              
ATOM    116  O   LYS B  40       1.547  45.877  22.680  1.00  0.00              
ATOM    117  N   LYS B  41       2.921  47.179  23.848  1.00  0.00              
ATOM    118  CA  LYS B  41       2.095  48.344  23.595  1.00  0.00              
ATOM    119  C   LYS B  41       2.128  48.733  22.128  1.00  0.00              
ATOM    120  O   LYS B  41       1.134  49.173  21.554  1.00  0.00              
ATOM    121  N   SER B  42       3.300  48.653  21.512  1.00  0.00              
ATOM    122  CA  SER B  42       3.415  48.985  20.108  1.00  0.00              
ATOM    123  C   SER B  42       2.641  47.983  19.269  1.00  0.00              
ATOM    124  O   SER B  42       1.747  48.353  18.509  1.00  0.00              
ATOM    125  N   ALA B  43       2.649  46.730  19.706  1.00  0.00              
ATOM    126  CA  ALA B  43       1.943  45.708  18.973  1.00  0.00              
ATOM    127  C   ALA B  43       0.486  45.636  19.369  1.00  0.00              
ATOM    128  O   ALA B  43      -0.298  44.909  18.775  1.00  0.00              
ATOM    129  N   HIS B  44       0.090  46.271  20.454  1.00  0.00              
ATOM    130  CA  HIS B  44      -1.308  46.192  20.819  1.00  0.00              
ATOM    131  C   HIS B  44      -2.093  47.382  20.288  1.00  0.00              
ATOM    132  O   HIS B  44      -3.272  47.553  20.604  1.00  0.00              
END
