REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0074AL074_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : STERNBERG 
REMARK  ---------------------------------------------------------- 
TARGET T0074  
AUTHOR 3873-9906-1225  
REMARK Submission 2  
REMARK Work by Gidon Moont (1) , Lawrence Kelley (1),  
REMARK Bob MacCallum (1), Marcel Turcotte (1) Mansoor Saqi (2)  
REMARK and Michael Sternberg (1) (m.sternberg@icrf.icnet.uk)  
REMARK (1) Biomolecular Modelling Laboratory,  
REMARK Imperial Cancer Research Fund  
REMARK (1) Lincoln's Inn Fields, London WC2A 3PX, UK  
REMARK (2) Bioinformatics Group, GlaxoWellcome, Stevenage, UK  
METHOD  
METHOD Method outline  
METHOD ---------------  
METHOD unknown = target, library of known folds = template  
METHOD (0) Initial check for remote homology of target  
METHOD to templates of known structures using PSI-BLAST  
METHOD (1) Secondary structure & sequence target against fold  
METHOD template library using FOLDFIT  
METHOD (2) Multiple structure / multiple sequence matching  
METHOD  against fold template library (3D-PSSM) *** NEW METHOD***  
METHOD (3) Search against Hidden Markov Models for fold template  
METHOD library using SAM  
METHOD (4) Local hydrophobicity and predicted secondary structure  
METHOD matched for target and template using SIVA (MacCallum &  
METHOD Thornton)  
METHOD (6) Evaluation of above results in terms of literature and  
METHOD function of target.  
METHOD  
METHOD General features of approach  
METHOD -----------------------------  
METHOD  
METHOD (i) The fold (template) library consists of non-redundant  
METHOD SCOP domains with <40% sequence identity per family (called  
METHOD SCOP40).  
METHOD  
METHOD (ii) Secondary structure prediction from multiple alignment  
METHOD (homologues gathered with PSI-BLAST) DSC (King &  
METHOD Sternberg); PHD (Rost & Sander); JPRED (Barton)  
METHOD  
METHOD Method details  
METHOD --------------  
METHOD  
METHOD (1) FOLDFIT (Russell,R.B., Saqi, M.A.S., Bates,P.A.,  
METHOD Sayle,R.A.  & Sternberg, M.J.E. (1998). Prot Eng 11, 1-9.)  
METHOD The target is represented by sequence and predicted  
METHOD secondary structure and scanned against known secondary  
METHOD structure and sequence for template in fold library.  
METHOD Different weights for secondary structure and sequence are  
METHOD used to obtain different possible top hits.  
METHOD  
METHOD (2) 3D-PSSM - Structures within the same SCOP fold family  
METHOD are aligned in 3D and if structures can be superposed well  
METHOD then each is used together with all homologous  
METHOD sequences in sequence database found by PSI-BLAST.  
METHOD These 3D-PSSMs were generated for each template.  
METHOD The target is matched against each template,  
METHOD (3D-PSSM, Kelley, MacCallum, Saqi & Sternberg, unpublished).  
METHOD NOW INCLUDING PREDICTED SECONDARY STRUCTURE  
METHOD as in FOLDFIT.  
METHOD  
METHOD (3) HMM from SAM (Hughley & Krogh ) against a  
METHOD library generated from each  
METHOD template in SCOP40 (Moont, MacCallum & Sternberg).  
METHOD  
METHOD (4) Vector-based alignment of per-residue hydrophobicity  
METHOD and DSC predicted secondary structure probabilities for  
METHOD both target and template. This approach could also  
METHOD be used in the absence of known structures for library  
METHOD sequences.  Algorithm is SIVA (MacCallum & Thornton,  
METHOD unpublished)  
METHOD  
METHOD  
METHOD (5) Visual inspection of results.  
METHOD  
METHOD details for t0074  
METHOD PSIBLAST, FOLDFIT, SIVA, 3DPSSM all identify  
METHOD the e-f hand proteins as top hit  
METHOD Automatic alignments with minor adjustement  
METHOD used to generate model  
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1osa 
ATOM      1  N   GLU   127     -18.676  33.035  34.875  1.00  0.00              
ATOM      2  CA  GLU   127     -17.320  33.098  35.406  1.00  0.00              
ATOM      3  C   GLU   127     -16.276  33.535  34.383  1.00  0.00              
ATOM      4  O   GLU   127     -15.313  34.206  34.738  1.00  0.00              
ATOM      5  N   ASP   128     -16.432  33.131  33.117  1.00  0.00              
ATOM      6  CA  ASP   128     -15.539  33.562  32.047  1.00  0.00              
ATOM      7  C   ASP   128     -15.651  35.056  31.740  1.00  0.00              
ATOM      8  O   ASP   128     -14.658  35.746  31.515  1.00  0.00              
ATOM      9  N   LYS   129     -16.911  35.499  31.712  1.00  0.00              
ATOM     10  CA  LYS   129     -17.301  36.898  31.562  1.00  0.00              
ATOM     11  C   LYS   129     -16.689  37.725  32.675  1.00  0.00              
ATOM     12  O   LYS   129     -16.096  38.764  32.399  1.00  0.00              
ATOM     13  N   ALA   130     -16.801  37.243  33.924  1.00  0.00              
ATOM     14  CA  ALA   130     -16.222  37.922  35.078  1.00  0.00              
ATOM     15  C   ALA   130     -14.719  38.075  34.951  1.00  0.00              
ATOM     16  O   ALA   130     -14.156  39.138  35.209  1.00  0.00              
ATOM     17  N   LYS   131     -14.050  37.022  34.478  1.00  0.00              
ATOM     18  CA  LYS   131     -12.616  37.106  34.227  1.00  0.00              
ATOM     19  C   LYS   131     -12.286  38.013  33.038  1.00  0.00              
ATOM     20  O   LYS   131     -11.247  38.672  33.039  1.00  0.00              
ATOM     21  N   TYR   132     -13.150  38.068  32.010  1.00  0.00              
ATOM     22  CA  TYR   132     -12.939  39.043  30.943  1.00  0.00              
ATOM     23  C   TYR   132     -13.214  40.480  31.397  1.00  0.00              
ATOM     24  O   TYR   132     -12.519  41.402  30.959  1.00  0.00              
ATOM     25  N   ASP   133     -14.169  40.710  32.317  1.00  0.00              
ATOM     26  CA  ASP   133     -14.263  42.019  32.944  1.00  0.00              
ATOM     27  C   ASP   133     -13.052  42.452  33.757  1.00  0.00              
ATOM     28  O   ASP   133     -12.706  43.630  33.731  1.00  0.00              
ATOM     29  N   ALA   134     -12.372  41.544  34.471  1.00  0.00              
ATOM     30  CA  ALA   134     -11.126  41.882  35.168  1.00  0.00              
ATOM     31  C   ALA   134      -9.980  42.400  34.309  1.00  0.00              
ATOM     32  O   ALA   134      -9.282  43.371  34.612  1.00  0.00              
ATOM     33  N   ILE   135      -9.824  41.700  33.190  1.00  0.00              
ATOM     34  CA  ILE   135      -8.860  42.073  32.179  1.00  0.00              
ATOM     35  C   ILE   135      -9.184  43.431  31.537  1.00  0.00              
ATOM     36  O   ILE   135      -8.270  44.221  31.327  1.00  0.00              
ATOM     37  N   PHE   136     -10.463  43.722  31.250  1.00  0.00              
ATOM     38  CA  PHE   136     -10.899  44.979  30.639  1.00  0.00              
ATOM     39  C   PHE   136     -10.596  46.124  31.570  1.00  0.00              
ATOM     40  O   PHE   136     -10.153  47.195  31.166  1.00  0.00              
ATOM     41  N   ASP   137     -10.812  45.824  32.846  1.00  0.00              
ATOM     42  CA  ASP   137     -10.611  46.775  33.916  1.00  0.00              
ATOM     43  C   ASP   137      -9.177  47.199  34.092  1.00  0.00              
ATOM     44  O   ASP   137      -8.940  48.293  34.593  1.00  0.00              
ATOM     45  N   SER   138      -8.194  46.378  33.689  1.00  0.00              
ATOM     46  CA  SER   138      -6.790  46.756  33.790  1.00  0.00              
ATOM     47  C   SER   138      -6.466  47.905  32.843  1.00  0.00              
ATOM     48  O   SER   138      -5.754  48.846  33.175  1.00  0.00              
ATOM     49  N   LEU   139      -7.066  47.815  31.669  1.00  0.00              
ATOM     50  CA  LEU   139      -6.899  48.818  30.628  1.00  0.00              
ATOM     51  C   LEU   139      -7.781  50.043  30.837  1.00  0.00              
ATOM     52  O   LEU   139      -7.333  51.176  30.688  1.00  0.00              
ATOM     53  N   GLY   144     -15.870  52.672  30.806  1.00  0.00              
ATOM     54  CA  GLY   144     -16.397  51.594  29.991  1.00  0.00              
ATOM     55  C   GLY   144     -15.753  51.590  28.624  1.00  0.00              
ATOM     56  O   GLY   144     -16.294  50.969  27.717  1.00  0.00              
ATOM     57  N   PHE   145     -14.682  52.349  28.431  1.00  0.00              
ATOM     58  CA  PHE   145     -13.998  52.360  27.135  1.00  0.00              
ATOM     59  C   PHE   145     -12.519  52.433  27.448  1.00  0.00              
ATOM     60  O   PHE   145     -12.054  53.018  28.466  1.00  0.00              
ATOM     61  N   LEU   146     -11.782  51.906  26.408  1.00  0.00              
ATOM     62  CA  LEU   146     -10.315  51.952  26.397  1.00  0.00              
ATOM     63  C   LEU   146      -9.887  52.844  25.232  1.00  0.00              
ATOM     64  O   LEU   146     -10.278  52.626  24.068  1.00  0.00              
ATOM     65  N   SER   147      -9.090  53.834  25.515  1.00  0.00              
ATOM     66  CA  SER   147      -8.697  54.821  24.523  1.00  0.00              
ATOM     67  C   SER   147      -7.260  54.575  24.147  1.00  0.00              
ATOM     68  O   SER   147      -6.603  53.795  24.838  1.00  0.00              
ATOM     69  N   GLY   148      -6.691  55.288  23.159  1.00  0.00              
ATOM     70  CA  GLY   148      -5.288  55.049  22.802  1.00  0.00              
ATOM     71  C   GLY   148      -4.381  55.374  23.957  1.00  0.00              
ATOM     72  O   GLY   148      -3.365  54.725  24.145  1.00  0.00              
ATOM     73  N   ASP   149      -4.772  56.352  24.762  1.00  0.00              
ATOM     74  CA  ASP   149      -3.936  56.770  25.862  1.00  0.00              
ATOM     75  C   ASP   149      -3.970  55.852  27.065  1.00  0.00              
ATOM     76  O   ASP   149      -3.002  55.835  27.825  1.00  0.00              
ATOM     77  N   LYS   150      -5.068  55.110  27.262  1.00  0.00              
ATOM     78  CA  LYS   150      -5.138  54.076  28.294  1.00  0.00              
ATOM     79  C   LYS   150      -4.364  52.846  27.885  1.00  0.00              
ATOM     80  O   LYS   150      -3.637  52.272  28.687  1.00  0.00              
ATOM     81  N   VAL   151      -4.513  52.429  26.623  1.00  0.00              
ATOM     82  CA  VAL   151      -3.641  51.402  26.022  1.00  0.00              
ATOM     83  C   VAL   151      -2.136  51.674  26.204  1.00  0.00              
ATOM     84  O   VAL   151      -1.373  50.822  26.677  1.00  0.00              
ATOM     85  N   LYS   152      -1.773  52.941  25.949  1.00  0.00              
ATOM     86  CA  LYS   152      -0.435  53.472  26.137  1.00  0.00              
ATOM     87  C   LYS   152       0.093  53.341  27.552  1.00  0.00              
ATOM     88  O   LYS   152       1.247  52.946  27.701  1.00  0.00              
ATOM     89  N   PRO   153      -0.730  53.609  28.591  1.00  0.00              
ATOM     90  CA  PRO   153      -0.323  53.500  29.986  1.00  0.00              
ATOM     91  C   PRO   153      -0.015  52.063  30.377  1.00  0.00              
ATOM     92  O   PRO   153       0.895  51.827  31.182  1.00  0.00              
ATOM     93  N   VAL   154      -0.757  51.104  29.803  1.00  0.00              
ATOM     94  CA  VAL   154      -0.562  49.695  30.109  1.00  0.00              
ATOM     95  C   VAL   154       0.701  49.176  29.426  1.00  0.00              
ATOM     96  O   VAL   154       1.534  48.547  30.083  1.00  0.00              
ATOM     97  N   LEU   155       0.879  49.469  28.124  1.00  0.00              
ATOM     98  CA  LEU   155       2.080  49.095  27.367  1.00  0.00              
ATOM     99  C   LEU   155       3.367  49.597  28.017  1.00  0.00              
ATOM    100  O   LEU   155       4.283  48.822  28.293  1.00  0.00              
ATOM    101  N   LEU   156       3.441  50.899  28.333  1.00  0.00              
ATOM    102  CA  LEU   156       4.553  51.470  29.076  1.00  0.00              
ATOM    103  C   LEU   156       4.830  50.755  30.392  1.00  0.00              
ATOM    104  O   LEU   156       5.995  50.593  30.786  1.00  0.00              
ATOM    105  N   LYS   159       7.356  51.423  24.967  1.00  0.00              
ATOM    106  CA  LYS   159       6.830  52.773  24.869  1.00  0.00              
ATOM    107  C   LYS   159       6.438  53.146  23.441  1.00  0.00              
ATOM    108  O   LYS   159       7.223  53.783  22.723  1.00  0.00              
ATOM    109  N   LEU   160       5.222  52.771  22.989  1.00  0.00              
ATOM    110  CA  LEU   160       4.754  52.985  21.628  1.00  0.00              
ATOM    111  C   LEU   160       4.441  54.463  21.416  1.00  0.00              
ATOM    112  O   LEU   160       4.180  55.224  22.361  1.00  0.00              
ATOM    113  N   PRO   161       4.547  54.876  20.154  1.00  0.00              
ATOM    114  CA  PRO   161       4.158  56.215  19.770  1.00  0.00              
ATOM    115  C   PRO   161       2.658  56.152  19.563  1.00  0.00              
ATOM    116  O   PRO   161       2.064  55.089  19.317  1.00  0.00              
ATOM    117  N   VAL   162       2.108  57.363  19.562  1.00  0.00              
ATOM    118  CA  VAL   162       0.695  57.580  19.314  1.00  0.00              
ATOM    119  C   VAL   162       0.172  56.941  18.018  1.00  0.00              
ATOM    120  O   VAL   162      -0.883  56.299  18.021  1.00  0.00              
ATOM    121  N   ASP   163       0.928  57.002  16.912  1.00  0.00              
ATOM    122  CA  ASP   163       0.541  56.336  15.671  1.00  0.00              
ATOM    123  C   ASP   163       0.450  54.816  15.776  1.00  0.00              
ATOM    124  O   ASP   163      -0.437  54.167  15.223  1.00  0.00              
ATOM    125  N   ILE   164       1.378  54.222  16.538  1.00  0.00              
ATOM    126  CA  ILE   164       1.374  52.777  16.811  1.00  0.00              
ATOM    127  C   ILE   164       0.171  52.340  17.654  1.00  0.00              
ATOM    128  O   ILE   164      -0.481  51.324  17.398  1.00  0.00              
ATOM    129  N   LEU   165      -0.146  53.157  18.665  1.00  0.00              
ATOM    130  CA  LEU   165      -1.359  52.945  19.451  1.00  0.00              
ATOM    131  C   LEU   165      -2.668  53.012  18.675  1.00  0.00              
ATOM    132  O   LEU   165      -3.561  52.176  18.866  1.00  0.00              
ATOM    133  N   GLY   166      -2.752  53.964  17.722  1.00  0.00              
ATOM    134  CA  GLY   166      -3.917  54.102  16.859  1.00  0.00              
ATOM    135  C   GLY   166      -4.098  52.910  15.937  1.00  0.00              
ATOM    136  O   GLY   166      -5.240  52.494  15.688  1.00  0.00              
ATOM    137  N   ARG   167      -3.000  52.300  15.454  1.00  0.00              
ATOM    138  CA  ARG   167      -3.150  51.100  14.626  1.00  0.00              
ATOM    139  C   ARG   167      -3.684  49.891  15.400  1.00  0.00              
ATOM    140  O   ARG   167      -4.545  49.147  14.932  1.00  0.00              
ATOM    141  N   VAL   168      -3.213  49.714  16.629  1.00  0.00              
ATOM    142  CA  VAL   168      -3.745  48.694  17.532  1.00  0.00              
ATOM    143  C   VAL   168      -5.223  48.886  17.865  1.00  0.00              
ATOM    144  O   VAL   168      -5.950  47.891  17.846  1.00  0.00              
ATOM    145  N   TRP   169      -5.693  50.130  18.161  1.00  0.00              
ATOM    146  CA  TRP   169      -7.110  50.377  18.406  1.00  0.00              
ATOM    147  C   TRP   169      -7.895  50.137  17.125  1.00  0.00              
ATOM    148  O   TRP   169      -8.965  49.525  17.153  1.00  0.00              
ATOM    149  N   GLU   170      -7.396  50.562  15.941  1.00  0.00              
ATOM    150  CA  GLU   170      -8.201  50.454  14.710  1.00  0.00              
ATOM    151  C   GLU   170      -8.524  49.022  14.304  1.00  0.00              
ATOM    152  O   GLU   170      -9.571  48.679  13.747  1.00  0.00              
ATOM    153  N   LEU   171      -7.548  48.190  14.676  1.00  0.00              
ATOM    154  CA  LEU   171      -7.614  46.746  14.519  1.00  0.00              
ATOM    155  C   LEU   171      -8.807  46.123  15.252  1.00  0.00              
ATOM    156  O   LEU   171      -9.428  45.173  14.770  1.00  0.00              
ATOM    157  N   SER   172      -9.146  46.722  16.403  1.00  0.00              
ATOM    158  CA  SER   172     -10.117  46.155  17.334  1.00  0.00              
ATOM    159  C   SER   172     -11.416  46.947  17.284  1.00  0.00              
ATOM    160  O   SER   172     -12.478  46.437  17.642  1.00  0.00              
ATOM    161  N   ASP   173     -11.355  48.209  16.848  1.00  0.00              
ATOM    162  CA  ASP   173     -12.531  49.064  16.898  1.00  0.00              
ATOM    163  C   ASP   173     -13.585  48.758  15.852  1.00  0.00              
ATOM    164  O   ASP   173     -13.600  49.376  14.797  1.00  0.00              
ATOM    165  N   ILE   174     -14.524  47.851  16.121  1.00  0.00              
ATOM    166  CA  ILE   174     -15.445  47.406  15.084  1.00  0.00              
ATOM    167  C   ILE   174     -16.430  48.476  14.596  1.00  0.00              
ATOM    168  O   ILE   174     -16.667  48.584  13.394  1.00  0.00              
ATOM    169  N   ASP   175     -16.966  49.319  15.498  1.00  0.00              
ATOM    170  CA  ASP   175     -17.858  50.415  15.124  1.00  0.00              
ATOM    171  C   ASP   175     -17.197  51.736  14.757  1.00  0.00              
ATOM    172  O   ASP   175     -17.897  52.683  14.390  1.00  0.00              
ATOM    173  N   HIS   176     -15.881  51.887  14.885  1.00  0.00              
ATOM    174  CA  HIS   176     -15.204  53.054  14.337  1.00  0.00              
ATOM    175  C   HIS   176     -15.277  54.293  15.201  1.00  0.00              
ATOM    176  O   HIS   176     -14.967  55.383  14.710  1.00  0.00              
ATOM    177  N   ASP   177     -15.670  54.184  16.485  1.00  0.00              
ATOM    178  CA  ASP   177     -15.826  55.371  17.320  1.00  0.00              
ATOM    179  C   ASP   177     -14.564  55.820  18.022  1.00  0.00              
ATOM    180  O   ASP   177     -14.584  56.796  18.767  1.00  0.00              
ATOM    181  N   GLY   178     -13.460  55.123  17.737  1.00  0.00              
ATOM    182  CA  GLY   178     -12.141  55.514  18.199  1.00  0.00              
ATOM    183  C   GLY   178     -11.744  54.883  19.516  1.00  0.00              
ATOM    184  O   GLY   178     -10.658  55.122  20.050  1.00  0.00              
ATOM    185  N   MET   179     -12.685  54.117  20.081  1.00  0.00              
ATOM    186  CA  MET   179     -12.430  53.387  21.305  1.00  0.00              
ATOM    187  C   MET   179     -13.070  51.956  21.260  1.00  0.00              
ATOM    188  O   MET   179     -13.958  51.566  20.449  1.00  0.00              
ATOM    189  N   LEU   180     -12.553  51.177  22.249  1.00  0.00              
ATOM    190  CA  LEU   180     -12.881  49.752  22.418  1.00  0.00              
ATOM    191  C   LEU   180     -13.817  49.628  23.607  1.00  0.00              
ATOM    192  O   LEU   180     -13.380  50.045  24.675  1.00  0.00              
ATOM    193  N   ASP   181     -15.038  49.130  23.445  1.00  0.00              
ATOM    194  CA  ASP   181     -15.919  48.928  24.591  1.00  0.00              
ATOM    195  C   ASP   181     -15.783  47.498  25.072  1.00  0.00              
ATOM    196  O   ASP   181     -14.866  46.807  24.631  1.00  0.00              
ATOM    197  N   ARG   182     -16.625  46.976  25.972  1.00  0.00              
ATOM    198  CA  ARG   182     -16.420  45.604  26.408  1.00  0.00              
ATOM    199  C   ARG   182     -16.852  44.539  25.379  1.00  0.00              
ATOM    200  O   ARG   182     -16.119  43.551  25.238  1.00  0.00              
ATOM    201  N   ASP   183     -17.946  44.598  24.633  1.00  0.00              
ATOM    202  CA  ASP   183     -18.239  43.698  23.523  1.00  0.00              
ATOM    203  C   ASP   183     -17.106  43.592  22.513  1.00  0.00              
ATOM    204  O   ASP   183     -16.786  42.504  22.020  1.00  0.00              
ATOM    205  N   GLU   184     -16.464  44.723  22.226  1.00  0.00              
ATOM    206  CA  GLU   184     -15.341  44.721  21.277  1.00  0.00              
ATOM    207  C   GLU   184     -14.127  44.003  21.838  1.00  0.00              
ATOM    208  O   GLU   184     -13.410  43.305  21.126  1.00  0.00              
ATOM    209  N   PHE   185     -13.899  44.130  23.134  1.00  0.00              
ATOM    210  CA  PHE   185     -12.782  43.451  23.759  1.00  0.00              
ATOM    211  C   PHE   185     -13.085  41.976  23.894  1.00  0.00              
ATOM    212  O   PHE   185     -12.160  41.176  23.831  1.00  0.00              
END
