REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL019_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0065  
AUTHOR 9070-5088-8627  
REMARK   
REMARK Prediction date: Monday July 29, 1998  
REMARK Group name: UCSC-compbio  
REMARK Authors: Christian Barrett, Melissa Cline, Mark Diekens, Leslie Grate,  
REMARK 	 Kevin Karplus, David Haussler and Richard Hughey  
REMARK University of California, Santa Cruz  
REMARK   
METHOD Overview  
METHOD   
METHOD Fold recognition was performed using the Target98 (SAM-T98) method  
METHOD [3] using SAM version 2.1.1 [1], a refinement of the methods developed  
METHOD by this group for CASP2 [2].  This method attempts to find and multiply   
METHOD align a set of homologs to a given sequence, then create an HMM from that   
METHOD multiple alignment.  
METHOD   
METHOD First, a set of sequence weights is determined from the alignment.  Next,   
METHOD Modelfromalign is used to build the model from the alignment and the   
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring   
METHOD of the sequences, using a reversed-sequence normalization feature.  
METHOD   
METHOD The weighting method, detailed in upcoming publications [3,4],  
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an  
METHOD entropy method to set the final weights.  
METHOD   
METHOD Alignment generation  
METHOD   
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set  
METHOD of very close homologs, and once to produce a set of possible homologs.  
METHOD   
METHOD The method then uses multiple iterations of a selection, training, and   
METHOD alignment procedure.  Each iteration involves an initial alignment, a set   
METHOD of search sequences, a threshold value, and a transition regularizer.   
METHOD   
METHOD The first iteration uses a single sequence (or seed alignment) as the   
METHOD initial alignment and the close homologs found by BLASTP are used as the   
METHOD search set.  The threshold is set very strictly, so that only good matches   
METHOD to the sequence are considered.  This iteration uses a transition regularizer   
METHOD that was designed to match the gap costs used by BLASTP.  
METHOD   
METHOD On subsequent iterations the input alignment is the output from the  
METHOD previous iteration, the search set is the larger set of possible  
METHOD homologs found by BLASTP, and the thresholds are gradually loosened.  
METHOD The second through second-from-last iteration use a ``long-match''  
METHOD transition regularizer, and the final iteration uses a transition regularizer   
METHOD trained on FSSP alignments.  
METHOD   
METHOD References  
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996.  
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.    
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R.  
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and   
METHOD     Genetics, Suppl. 1, 134-9, 1997.  
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06,  
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998.  
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard,  
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998.  
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994.  
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S.  
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996.  
METHOD   
METHOD   
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ois 
ATOM      1  N   ASN B   3      -8.098  72.008  52.500  1.00  0.00              
ATOM      2  CA  ASN B   3      -8.864  71.197  51.502  1.00  0.00              
ATOM      3  C   ASN B   3      -8.953  69.711  51.896  1.00  0.00              
ATOM      4  O   ASN B   3     -10.044  69.196  52.104  1.00  0.00              
ATOM      5  N   ALA B   4      -7.813  69.051  52.069  1.00  0.00              
ATOM      6  CA  ALA B   4      -7.791  67.635  52.444  1.00  0.00              
ATOM      7  C   ALA B   4      -8.663  67.343  53.654  1.00  0.00              
ATOM      8  O   ALA B   4      -9.629  66.590  53.568  1.00  0.00              
ATOM      9  N   LYS B   5      -8.353  67.995  54.768  1.00  0.00              
ATOM     10  CA  LYS B   5      -9.099  67.800  56.007  1.00  0.00              
ATOM     11  C   LYS B   5     -10.576  68.210  55.891  1.00  0.00              
ATOM     12  O   LYS B   5     -11.442  67.582  56.497  1.00  0.00              
ATOM     13  N   GLN B   6     -10.873  69.211  55.064  1.00  0.00              
ATOM     14  CA  GLN B   6     -12.257  69.640  54.884  1.00  0.00              
ATOM     15  C   GLN B   6     -13.012  68.477  54.237  1.00  0.00              
ATOM     16  O   GLN B   6     -14.082  68.089  54.706  1.00  0.00              
ATOM     17  N   GLU B   7     -12.433  67.907  53.181  1.00  0.00              
ATOM     18  CA  GLU B   7     -13.031  66.768  52.484  1.00  0.00              
ATOM     19  C   GLU B   7     -13.197  65.639  53.504  1.00  0.00              
ATOM     20  O   GLU B   7     -14.228  64.963  53.547  1.00  0.00              
ATOM     21  N   HIS B   8     -12.165  65.465  54.325  1.00  0.00              
ATOM     22  CA  HIS B   8     -12.131  64.453  55.368  1.00  0.00              
ATOM     23  C   HIS B   8     -13.360  64.642  56.260  1.00  0.00              
ATOM     24  O   HIS B   8     -13.982  63.669  56.685  1.00  0.00              
ATOM     25  N   PHE B   9     -13.740  65.899  56.475  1.00  0.00              
ATOM     26  CA  PHE B   9     -14.874  66.241  57.318  1.00  0.00              
ATOM     27  C   PHE B   9     -16.230  66.072  56.644  1.00  0.00              
ATOM     28  O   PHE B   9     -17.191  65.589  57.268  1.00  0.00              
ATOM     29  N   GLU B  10     -16.322  66.493  55.387  1.00  0.00              
ATOM     30  CA  GLU B  10     -17.572  66.375  54.642  1.00  0.00              
ATOM     31  C   GLU B  10     -17.912  64.904  54.377  1.00  0.00              
ATOM     32  O   GLU B  10     -19.091  64.540  54.304  1.00  0.00              
ATOM     33  N   LEU B  11     -16.874  64.066  54.313  1.00  0.00              
ATOM     34  CA  LEU B  11     -17.014  62.635  54.080  1.00  0.00              
ATOM     35  C   LEU B  11     -17.497  61.908  55.327  1.00  0.00              
ATOM     36  O   LEU B  11     -18.504  61.226  55.304  1.00  0.00              
ATOM     37  N   ASP B  12     -16.768  62.052  56.419  1.00  0.00              
ATOM     38  CA  ASP B  12     -17.117  61.399  57.672  1.00  0.00              
ATOM     39  C   ASP B  12     -18.494  61.852  58.193  1.00  0.00              
ATOM     40  O   ASP B  12     -19.198  61.094  58.870  1.00  0.00              
ATOM     41  N   GLN B  13     -18.885  63.079  57.867  1.00  0.00              
ATOM     42  CA  GLN B  13     -20.190  63.579  58.272  1.00  0.00              
ATOM     43  C   GLN B  13     -21.251  62.798  57.464  1.00  0.00              
ATOM     44  O   GLN B  13     -22.287  62.380  57.989  1.00  0.00              
ATOM     45  N   GLU B  14     -20.964  62.565  56.190  1.00  0.00              
ATOM     46  CA  GLU B  14     -21.871  61.815  55.345  1.00  0.00              
ATOM     47  C   GLU B  14     -21.927  60.358  55.789  1.00  0.00              
ATOM     48  O   GLU B  14     -23.001  59.775  55.905  1.00  0.00              
ATOM     49  N   TRP B  15     -20.762  59.773  56.028  1.00  0.00              
ATOM     50  CA  TRP B  15     -20.651  58.384  56.451  1.00  0.00              
ATOM     51  C   TRP B  15     -21.170  58.105  57.865  1.00  0.00              
ATOM     52  O   TRP B  15     -21.262  56.943  58.272  1.00  0.00              
ATOM     53  N   VAL B  16     -21.508  59.163  58.604  1.00  0.00              
ATOM     54  CA  VAL B  16     -22.025  59.042  59.966  1.00  0.00              
ATOM     55  C   VAL B  16     -23.270  58.143  60.005  1.00  0.00              
ATOM     56  O   VAL B  16     -23.414  57.288  60.886  1.00  0.00              
ATOM     57  N   GLU B  17     -24.101  58.276  58.977  1.00  0.00              
ATOM     58  CA  GLU B  17     -25.343  57.530  58.856  1.00  0.00              
ATOM     59  C   GLU B  17     -25.144  56.039  58.573  1.00  0.00              
ATOM     60  O   GLU B  17     -26.013  55.227  58.874  1.00  0.00              
ATOM     61  N   LEU B  18     -23.994  55.674  58.018  1.00  0.00              
ATOM     62  CA  LEU B  18     -23.714  54.276  57.692  1.00  0.00              
ATOM     63  C   LEU B  18     -22.778  53.578  58.666  1.00  0.00              
ATOM     64  O   LEU B  18     -22.744  52.342  58.750  1.00  0.00              
ATOM     65  N   MET B  19     -21.994  54.368  59.384  1.00  0.00              
ATOM     66  CA  MET B  19     -21.019  53.825  60.320  1.00  0.00              
ATOM     67  C   MET B  19     -21.669  53.257  61.590  1.00  0.00              
ATOM     68  O   MET B  19     -21.034  52.517  62.351  1.00  0.00              
ATOM     69  N   VAL B  20     -22.936  53.602  61.804  1.00  0.00              
ATOM     70  CA  VAL B  20     -23.651  53.165  62.988  1.00  0.00              
ATOM     71  C   VAL B  20     -25.053  52.705  62.629  1.00  0.00              
ATOM     72  O   VAL B  20     -25.678  53.197  61.687  1.00  0.00              
ATOM     73  N   ALA B  25     -18.847  47.910  60.575  1.00  0.00              
ATOM     74  CA  ALA B  25     -17.620  47.934  59.793  1.00  0.00              
ATOM     75  C   ALA B  25     -17.962  47.357  58.418  1.00  0.00              
ATOM     76  O   ALA B  25     -18.654  46.333  58.354  1.00  0.00              
ATOM     77  N   ASN B  26     -17.527  48.001  57.335  1.00  0.00              
ATOM     78  CA  ASN B  26     -17.781  47.536  55.951  1.00  0.00              
ATOM     79  C   ASN B  26     -19.013  48.123  55.264  1.00  0.00              
ATOM     80  O   ASN B  26     -19.588  47.478  54.397  1.00  0.00              
ATOM     81  N   ILE B  27     -19.376  49.362  55.568  1.00  0.00              
ATOM     82  CA  ILE B  27     -20.573  49.962  54.962  1.00  0.00              
ATOM     83  C   ILE B  27     -20.368  50.476  53.551  1.00  0.00              
ATOM     84  O   ILE B  27     -21.246  51.081  52.977  1.00  0.00              
ATOM     85  N   SER B  28     -19.180  50.283  53.016  1.00  0.00              
ATOM     86  CA  SER B  28     -18.867  50.737  51.670  1.00  0.00              
ATOM     87  C   SER B  28     -18.647  49.543  50.733  1.00  0.00              
ATOM     88  O   SER B  28     -17.987  48.564  51.093  1.00  0.00              
ATOM     89  N   PRO B  29     -19.277  49.578  49.566  1.00  0.00              
ATOM     90  CA  PRO B  29     -19.082  48.486  48.644  1.00  0.00              
ATOM     91  C   PRO B  29     -17.858  48.846  47.817  1.00  0.00              
ATOM     92  O   PRO B  29     -17.679  49.993  47.392  1.00  0.00              
ATOM     93  N   GLU B  30     -16.965  47.879  47.677  1.00  0.00              
ATOM     94  CA  GLU B  30     -15.720  48.066  46.924  1.00  0.00              
ATOM     95  C   GLU B  30     -15.975  48.420  45.468  1.00  0.00              
ATOM     96  O   GLU B  30     -16.857  47.867  44.830  1.00  0.00              
ATOM     97  N   GLU B  31     -15.215  49.376  44.942  1.00  0.00              
ATOM     98  CA  GLU B  31     -15.329  49.835  43.554  1.00  0.00              
ATOM     99  C   GLU B  31     -14.822  48.785  42.551  1.00  0.00              
ATOM    100  O   GLU B  31     -13.919  47.995  42.858  1.00  0.00              
ATOM    101  N   ILE B  32     -15.373  48.795  41.322  1.00  0.00              
ATOM    102  CA  ILE B  32     -14.910  47.815  40.334  1.00  0.00              
ATOM    103  C   ILE B  32     -13.428  48.063  40.016  1.00  0.00              
ATOM    104  O   ILE B  32     -12.915  49.173  40.229  1.00  0.00              
ATOM    105  N   ARG B  33     -12.736  47.026  39.547  1.00  0.00              
ATOM    106  CA  ARG B  33     -11.312  47.115  39.179  1.00  0.00              
ATOM    107  C   ARG B  33     -10.907  45.747  38.661  1.00  0.00              
ATOM    108  O   ARG B  33     -11.743  44.862  38.566  1.00  0.00              
ATOM    109  N   LEU B  37      -9.657  45.611  38.233  1.00  0.00              
ATOM    110  CA  LEU B  37      -9.139  44.323  37.792  1.00  0.00              
ATOM    111  C   LEU B  37      -8.580  43.599  39.038  1.00  0.00              
ATOM    112  O   LEU B  37      -7.953  44.232  39.923  1.00  0.00              
ATOM    113  N   LEU B  38      -8.910  42.310  39.137  1.00  0.00              
ATOM    114  CA  LEU B  38      -8.441  41.428  40.191  1.00  0.00              
ATOM    115  C   LEU B  38      -6.947  41.180  39.977  1.00  0.00              
ATOM    116  O   LEU B  38      -6.521  40.815  38.885  1.00  0.00              
ATOM    117  N   ASN B  39      -6.154  41.379  41.018  1.00  0.00              
ATOM    118  CA  ASN B  39      -4.736  41.164  40.943  1.00  0.00              
ATOM    119  C   ASN B  39      -4.445  39.912  41.779  1.00  0.00              
ATOM    120  O   ASN B  39      -4.629  39.901  43.000  1.00  0.00              
ATOM    121  N   LYS B  40      -4.106  38.822  41.104  1.00  0.00              
ATOM    122  CA  LYS B  40      -3.842  37.595  41.813  1.00  0.00              
ATOM    123  C   LYS B  40      -2.359  37.430  42.021  1.00  0.00              
ATOM    124  O   LYS B  40      -1.541  37.987  41.275  1.00  0.00              
ATOM    125  N   LYS B  41      -1.976  36.650  43.012  1.00  0.00              
ATOM    126  CA  LYS B  41      -0.560  36.516  43.206  1.00  0.00              
ATOM    127  C   LYS B  41      -0.007  35.306  42.484  1.00  0.00              
ATOM    128  O   LYS B  41      -0.749  34.361  42.190  1.00  0.00              
ATOM    129  N   SER B  42       1.255  35.430  42.063  1.00  0.00              
ATOM    130  CA  SER B  42       1.954  34.374  41.348  1.00  0.00              
ATOM    131  C   SER B  42       1.334  33.972  40.028  1.00  0.00              
ATOM    132  O   SER B  42       1.126  34.791  39.137  1.00  0.00              
ATOM    133  N   ALA B  43       1.080  32.682  39.895  1.00  0.00              
ATOM    134  CA  ALA B  43       0.473  32.123  38.709  1.00  0.00              
ATOM    135  C   ALA B  43      -1.051  32.019  38.885  1.00  0.00              
ATOM    136  O   ALA B  43      -1.661  31.076  38.398  1.00  0.00              
ATOM    137  N   HIS B  44      -1.670  32.965  39.589  1.00  0.00              
ATOM    138  CA  HIS B  44      -3.113  32.889  39.754  1.00  0.00              
ATOM    139  C   HIS B  44      -3.741  32.945  38.370  1.00  0.00              
ATOM    140  O   HIS B  44      -3.595  33.947  37.666  1.00  0.00              
ATOM    141  N   PRO B  45      -4.495  31.895  37.985  1.00  0.00              
ATOM    142  CA  PRO B  45      -5.122  31.873  36.666  1.00  0.00              
ATOM    143  C   PRO B  45      -6.210  32.918  36.388  1.00  0.00              
ATOM    144  O   PRO B  45      -6.564  33.140  35.238  1.00  0.00              
ATOM    145  N   GLY B  46      -6.717  33.587  37.413  1.00  0.00              
ATOM    146  CA  GLY B  46      -7.772  34.556  37.189  1.00  0.00              
ATOM    147  C   GLY B  46      -7.271  35.980  37.273  1.00  0.00              
ATOM    148  O   GLY B  46      -8.053  36.928  37.164  1.00  0.00              
ATOM    149  N   PRO B  47      -5.987  36.140  37.532  1.00  0.00              
ATOM    150  CA  PRO B  47      -5.430  37.482  37.625  1.00  0.00              
ATOM    151  C   PRO B  47      -5.748  38.297  36.347  1.00  0.00              
ATOM    152  O   PRO B  47      -5.634  37.804  35.216  1.00  0.00              
ATOM    153  N   ALA B  48      -6.223  39.516  36.542  1.00  0.00              
ATOM    154  CA  ALA B  48      -6.559  40.361  35.405  1.00  0.00              
ATOM    155  C   ALA B  48      -8.043  40.357  35.110  1.00  0.00              
ATOM    156  O   ALA B  48      -8.527  41.114  34.259  1.00  0.00              
ATOM    157  N   ALA B  49      -8.785  39.486  35.784  1.00  0.00              
ATOM    158  CA  ALA B  49     -10.213  39.466  35.540  1.00  0.00              
ATOM    159  C   ALA B  49     -10.894  40.666  36.187  1.00  0.00              
ATOM    160  O   ALA B  49     -10.432  41.175  37.200  1.00  0.00              
ATOM    161  N   ARG B  50     -11.928  41.182  35.533  1.00  0.00              
ATOM    162  CA  ARG B  50     -12.665  42.325  36.043  1.00  0.00              
ATOM    163  C   ARG B  50     -13.612  42.031  37.216  1.00  0.00              
ATOM    164  O   ARG B  50     -14.463  41.149  37.123  1.00  0.00              
ATOM    165  N   SER B  51     -13.432  42.727  38.326  1.00  0.00              
ATOM    166  CA  SER B  51     -14.335  42.622  39.489  1.00  0.00              
ATOM    167  C   SER B  51     -15.410  43.675  39.136  1.00  0.00              
ATOM    168  O   SER B  51     -15.137  44.884  39.035  1.00  0.00              
ATOM    169  N   HIS B  52     -16.604  43.203  38.814  1.00  0.00              
ATOM    170  CA  HIS B  52     -17.676  44.097  38.385  1.00  0.00              
ATOM    171  C   HIS B  52     -18.264  44.978  39.458  1.00  0.00              
ATOM    172  O   HIS B  52     -18.206  44.680  40.644  1.00  0.00              
ATOM    173  N   THR B  53     -18.798  46.107  39.018  1.00  0.00              
ATOM    174  CA  THR B  53     -19.418  47.054  39.924  1.00  0.00              
ATOM    175  C   THR B  53     -20.617  46.334  40.542  1.00  0.00              
ATOM    176  O   THR B  53     -21.406  45.705  39.826  1.00  0.00              
ATOM    177  N   VAL B  54     -20.761  46.465  41.856  1.00  0.00              
ATOM    178  CA  VAL B  54     -21.875  45.872  42.591  1.00  0.00              
ATOM    179  C   VAL B  54     -22.990  46.927  42.653  1.00  0.00              
ATOM    180  O   VAL B  54     -22.757  48.058  43.075  1.00  0.00              
ATOM    181  N   ASN B  55     -24.159  46.581  42.131  1.00  0.00              
ATOM    182  CA  ASN B  55     -25.320  47.478  42.126  1.00  0.00              
ATOM    183  C   ASN B  55     -26.304  47.070  43.243  1.00  0.00              
ATOM    184  O   ASN B  55     -26.192  45.977  43.799  1.00  0.00              
ATOM    185  N   PRO B  56     -27.276  47.946  43.581  1.00  0.00              
ATOM    186  CA  PRO B  56     -28.297  47.709  44.629  1.00  0.00              
ATOM    187  C   PRO B  56     -29.041  46.396  44.412  1.00  0.00              
ATOM    188  O   PRO B  56     -29.372  45.668  45.354  1.00  0.00              
END
