REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0064AL019_1_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0064  
AUTHOR 9070-5088-8627  
REMARK   
REMARK Prediction date: Thursday July 30, 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   ASP A  63      -2.526  38.062  32.860  1.00  0.00              
ATOM      2  CA  ASP A  63      -3.258  39.243  33.318  1.00  0.00              
ATOM      3  C   ASP A  63      -3.838  39.946  32.083  1.00  0.00              
ATOM      4  O   ASP A  63      -5.034  40.261  32.040  1.00  0.00              
ATOM      5  N   GLU A  64      -2.999  40.099  31.053  1.00  0.00              
ATOM      6  CA  GLU A  64      -3.387  40.758  29.818  1.00  0.00              
ATOM      7  C   GLU A  64      -4.525  39.993  29.151  1.00  0.00              
ATOM      8  O   GLU A  64      -5.479  40.597  28.675  1.00  0.00              
ATOM      9  N   LYS A  65      -4.404  38.668  29.089  1.00  0.00              
ATOM     10  CA  LYS A  65      -5.437  37.797  28.491  1.00  0.00              
ATOM     11  C   LYS A  65      -6.801  37.936  29.182  1.00  0.00              
ATOM     12  O   LYS A  65      -7.822  38.185  28.531  1.00  0.00              
ATOM     13  N   HIS A  66      -6.807  37.746  30.499  1.00  0.00              
ATOM     14  CA  HIS A  66      -8.037  37.852  31.308  1.00  0.00              
ATOM     15  C   HIS A  66      -8.680  39.246  31.202  1.00  0.00              
ATOM     16  O   HIS A  66      -9.888  39.376  30.966  1.00  0.00              
ATOM     17  N   GLU A  67      -7.862  40.291  31.315  1.00  0.00              
ATOM     18  CA  GLU A  67      -8.358  41.660  31.192  1.00  0.00              
ATOM     19  C   GLU A  67      -9.005  41.854  29.833  1.00  0.00              
ATOM     20  O   GLU A  67     -10.122  42.364  29.728  1.00  0.00              
ATOM     21  N   THR A  68      -8.306  41.415  28.789  1.00  0.00              
ATOM     22  CA  THR A  68      -8.774  41.609  27.430  1.00  0.00              
ATOM     23  C   THR A  68     -10.054  40.883  27.090  1.00  0.00              
ATOM     24  O   THR A  68     -10.948  41.429  26.425  1.00  0.00              
ATOM     25  N   GLU A  69     -10.166  39.650  27.558  1.00  0.00              
ATOM     26  CA  GLU A  69     -11.380  38.893  27.321  1.00  0.00              
ATOM     27  C   GLU A  69     -12.524  39.563  28.076  1.00  0.00              
ATOM     28  O   GLU A  69     -13.614  39.725  27.518  1.00  0.00              
ATOM     29  N   TYR A  70     -12.274  40.047  29.297  1.00  0.00              
ATOM     30  CA  TYR A  70     -13.338  40.730  30.028  1.00  0.00              
ATOM     31  C   TYR A  70     -13.690  42.063  29.399  1.00  0.00              
ATOM     32  O   TYR A  70     -14.870  42.420  29.325  1.00  0.00              
ATOM     33  N   ASP A  71     -12.678  42.745  28.860  1.00  0.00              
ATOM     34  CA  ASP A  71     -12.848  44.031  28.178  1.00  0.00              
ATOM     35  C   ASP A  71     -13.708  43.845  26.931  1.00  0.00              
ATOM     36  O   ASP A  71     -14.617  44.647  26.665  1.00  0.00              
ATOM     37  N   GLY A  72     -13.435  42.780  26.179  1.00  0.00              
ATOM     38  CA  GLY A  72     -14.205  42.491  24.968  1.00  0.00              
ATOM     39  C   GLY A  72     -15.650  42.148  25.305  1.00  0.00              
ATOM     40  O   GLY A  72     -16.587  42.493  24.549  1.00  0.00              
ATOM     41  N   GLN A  73     -15.830  41.500  26.450  1.00  0.00              
ATOM     42  CA  GLN A  73     -17.159  41.121  26.906  1.00  0.00              
ATOM     43  C   GLN A  73     -17.962  42.372  27.274  1.00  0.00              
ATOM     44  O   GLN A  73     -19.139  42.483  26.897  1.00  0.00              
ATOM     45  N   LEU A  74     -17.340  43.313  27.990  1.00  0.00              
ATOM     46  CA  LEU A  74     -18.028  44.548  28.356  1.00  0.00              
ATOM     47  C   LEU A  74     -18.281  45.371  27.097  1.00  0.00              
ATOM     48  O   LEU A  74     -19.327  46.024  26.964  1.00  0.00              
ATOM     49  N   ASP A  75     -17.323  45.324  26.170  1.00  0.00              
ATOM     50  CA  ASP A  75     -17.427  46.054  24.909  1.00  0.00              
ATOM     51  C   ASP A  75     -18.655  45.589  24.158  1.00  0.00              
ATOM     52  O   ASP A  75     -19.421  46.421  23.661  1.00  0.00              
ATOM     53  N   SER A  76     -18.818  44.264  24.066  1.00  0.00              
ATOM     54  CA  SER A  76     -19.979  43.647  23.410  1.00  0.00              
ATOM     55  C   SER A  76     -21.281  44.060  24.098  1.00  0.00              
ATOM     56  O   SER A  76     -22.227  44.450  23.452  1.00  0.00              
ATOM     57  N   GLU A  77     -21.318  43.982  25.415  1.00  0.00              
ATOM     58  CA  GLU A  77     -22.520  44.329  26.170  1.00  0.00              
ATOM     59  C   GLU A  77     -22.934  45.768  25.958  1.00  0.00              
ATOM     60  O   GLU A  77     -24.119  46.081  25.995  1.00  0.00              
ATOM     61  N   TRP A  78     -21.949  46.636  25.753  1.00  0.00              
ATOM     62  CA  TRP A  78     -22.177  48.063  25.553  1.00  0.00              
ATOM     63  C   TRP A  78     -22.476  48.451  24.118  1.00  0.00              
ATOM     64  O   TRP A  78     -22.579  49.623  23.814  1.00  0.00              
ATOM     65  N   GLU A  79     -22.535  47.494  23.217  1.00  0.00              
ATOM     66  CA  GLU A  79     -22.817  47.839  21.839  1.00  0.00              
ATOM     67  C   GLU A  79     -21.602  48.168  20.978  1.00  0.00              
ATOM     68  O   GLU A  79     -21.777  48.572  19.830  1.00  0.00              
ATOM     69  N   LYS A  80     -20.385  47.980  21.495  1.00  0.00              
ATOM     70  CA  LYS A  80     -19.185  48.269  20.709  1.00  0.00              
ATOM     71  C   LYS A  80     -18.749  49.731  20.611  1.00  0.00              
ATOM     72  O   LYS A  80     -19.401  50.612  21.178  1.00  0.00              
ATOM     73  N   LEU A  81     -17.614  50.020  19.938  1.00  0.00              
ATOM     74  CA  LEU A  81     -17.104  51.391  19.779  1.00  0.00              
ATOM     75  C   LEU A  81     -18.067  52.235  18.938  1.00  0.00              
ATOM     76  O   LEU A  81     -18.760  51.717  18.057  1.00  0.00              
ATOM     77  N   VAL A  82     -18.031  53.543  19.157  1.00  0.00              
ATOM     78  CA  VAL A  82     -18.909  54.472  18.467  1.00  0.00              
ATOM     79  C   VAL A  82     -18.418  54.920  17.088  1.00  0.00              
ATOM     80  O   VAL A  82     -19.228  55.245  16.216  1.00  0.00              
ATOM     81  N   ARG A  83     -17.104  54.932  16.883  1.00  0.00              
ATOM     82  CA  ARG A  83     -16.534  55.324  15.587  1.00  0.00              
ATOM     83  C   ARG A  83     -16.105  54.126  14.745  1.00  0.00              
ATOM     84  O   ARG A  83     -15.126  54.201  14.000  1.00  0.00              
ATOM     85  N   ASP A  84     -16.836  53.025  14.890  1.00  0.00              
ATOM     86  CA  ASP A  84     -16.562  51.813  14.143  1.00  0.00              
ATOM     87  C   ASP A  84     -15.120  51.363  13.947  1.00  0.00              
ATOM     88  O   ASP A  84     -14.648  51.291  12.811  1.00  0.00              
ATOM     89  N   ALA A  85     -14.427  51.011  15.025  1.00  0.00              
ATOM     90  CA  ALA A  85     -13.053  50.557  14.874  1.00  0.00              
ATOM     91  C   ALA A  85     -12.832  49.046  14.936  1.00  0.00              
ATOM     92  O   ALA A  85     -11.948  48.530  14.248  1.00  0.00              
ATOM     93  N   MET A  86     -13.629  48.337  15.727  1.00  0.00              
ATOM     94  CA  MET A  86     -13.495  46.882  15.862  1.00  0.00              
ATOM     95  C   MET A  86     -12.193  46.450  16.541  1.00  0.00              
ATOM     96  O   MET A  86     -11.145  46.311  15.910  1.00  0.00              
ATOM     97  N   THR A  87     -12.284  46.228  17.845  1.00  0.00              
ATOM     98  CA  THR A  87     -11.140  45.819  18.638  1.00  0.00              
ATOM     99  C   THR A  87     -11.116  44.293  18.721  1.00  0.00              
ATOM    100  O   THR A  87     -12.037  43.669  19.265  1.00  0.00              
ATOM    101  N   SER A  88     -10.112  43.690  18.095  1.00  0.00              
ATOM    102  CA  SER A  88      -9.977  42.247  18.098  1.00  0.00              
ATOM    103  C   SER A  88      -8.698  41.742  18.796  1.00  0.00              
ATOM    104  O   SER A  88      -8.662  40.614  19.284  1.00  0.00              
ATOM    105  N   GLY A  89      -7.654  42.568  18.859  1.00  0.00              
ATOM    106  CA  GLY A  89      -6.399  42.115  19.436  1.00  0.00              
ATOM    107  C   GLY A  89      -5.811  43.026  20.480  1.00  0.00              
ATOM    108  O   GLY A  89      -5.723  44.249  20.286  1.00  0.00              
ATOM    109  N   VAL A  90      -5.333  42.402  21.557  1.00  0.00              
ATOM    110  CA  VAL A  90      -4.730  43.136  22.657  1.00  0.00              
ATOM    111  C   VAL A  90      -3.528  43.937  22.194  1.00  0.00              
ATOM    112  O   VAL A  90      -3.383  45.109  22.531  1.00  0.00              
ATOM    113  N   SER A  91      -2.667  43.291  21.423  1.00  0.00              
ATOM    114  CA  SER A  91      -1.447  43.900  20.948  1.00  0.00              
ATOM    115  C   SER A  91      -1.609  45.148  20.101  1.00  0.00              
ATOM    116  O   SER A  91      -0.658  45.900  19.930  1.00  0.00              
ATOM    117  N   LYS A  92      -2.788  45.352  19.532  1.00  0.00              
ATOM    118  CA  LYS A  92      -3.017  46.521  18.698  1.00  0.00              
ATOM    119  C   LYS A  92      -3.544  47.677  19.526  1.00  0.00              
ATOM    120  O   LYS A  92      -3.782  48.758  18.996  1.00  0.00              
ATOM    121  N   LYS A  93      -3.742  47.428  20.820  1.00  0.00              
ATOM    122  CA  LYS A  93      -4.234  48.425  21.759  1.00  0.00              
ATOM    123  C   LYS A  93      -3.080  49.212  22.344  1.00  0.00              
ATOM    124  O   LYS A  93      -2.030  48.643  22.672  1.00  0.00              
ATOM    125  N   GLN A  94      -3.282  50.517  22.481  1.00  0.00              
ATOM    126  CA  GLN A  94      -2.261  51.395  23.034  1.00  0.00              
ATOM    127  C   GLN A  94      -2.957  52.221  24.110  1.00  0.00              
ATOM    128  O   GLN A  94      -3.865  53.016  23.844  1.00  0.00              
ATOM    129  N   PHE A  95      -2.563  51.945  25.343  1.00  0.00              
ATOM    130  CA  PHE A  95      -3.096  52.585  26.528  1.00  0.00              
ATOM    131  C   PHE A  95      -2.247  53.741  27.072  1.00  0.00              
ATOM    132  O   PHE A  95      -2.584  54.307  28.099  1.00  0.00              
ATOM    133  N   ARG A  96      -1.158  54.089  26.389  1.00  0.00              
ATOM    134  CA  ARG A  96      -0.236  55.121  26.869  1.00  0.00              
ATOM    135  C   ARG A  96      -0.799  56.488  27.283  1.00  0.00              
ATOM    136  O   ARG A  96      -0.470  57.001  28.353  1.00  0.00              
ATOM    137  N   GLU A  97      -1.651  57.062  26.443  1.00  0.00              
ATOM    138  CA  GLU A  97      -2.275  58.358  26.713  1.00  0.00              
ATOM    139  C   GLU A  97      -3.208  58.263  27.940  1.00  0.00              
ATOM    140  O   GLU A  97      -3.251  59.160  28.787  1.00  0.00              
ATOM    141  N   PHE A  98      -3.917  57.143  28.054  1.00  0.00              
ATOM    142  CA  PHE A  98      -4.777  56.924  29.193  1.00  0.00              
ATOM    143  C   PHE A  98      -3.889  56.839  30.440  1.00  0.00              
ATOM    144  O   PHE A  98      -4.182  57.481  31.470  1.00  0.00              
ATOM    145  N   LEU A  99      -2.802  56.066  30.358  1.00  0.00              
ATOM    146  CA  LEU A  99      -1.891  55.941  31.502  1.00  0.00              
ATOM    147  C   LEU A  99      -1.300  57.307  31.926  1.00  0.00              
ATOM    148  O   LEU A  99      -1.315  57.676  33.111  1.00  0.00              
ATOM    149  N   ASP A 100      -0.791  58.056  30.950  1.00  0.00              
ATOM    150  CA  ASP A 100      -0.184  59.355  31.219  1.00  0.00              
ATOM    151  C   ASP A 100      -1.183  60.323  31.841  1.00  0.00              
ATOM    152  O   ASP A 100      -0.834  61.148  32.701  1.00  0.00              
ATOM    153  N   TYR A 101      -2.432  60.209  31.418  1.00  0.00              
ATOM    154  CA  TYR A 101      -3.475  61.061  31.948  1.00  0.00              
ATOM    155  C   TYR A 101      -3.747  60.714  33.417  1.00  0.00              
ATOM    156  O   TYR A 101      -3.964  61.593  34.265  1.00  0.00              
ATOM    157  N   GLN A 102      -3.801  59.424  33.704  1.00  0.00              
ATOM    158  CA  GLN A 102      -4.022  58.982  35.061  1.00  0.00              
ATOM    159  C   GLN A 102      -2.884  59.471  35.961  1.00  0.00              
ATOM    160  O   GLN A 102      -3.130  60.012  37.042  1.00  0.00              
ATOM    161  N   LYS A 103      -1.647  59.353  35.484  1.00  0.00              
ATOM    162  CA  LYS A 103      -0.485  59.809  36.251  1.00  0.00              
ATOM    163  C   LYS A 103      -0.594  61.305  36.498  1.00  0.00              
ATOM    164  O   LYS A 103      -0.315  61.757  37.608  1.00  0.00              
ATOM    165  N   TRP A 104      -1.026  62.051  35.469  1.00  0.00              
ATOM    166  CA  TRP A 104      -1.219  63.507  35.544  1.00  0.00              
ATOM    167  C   TRP A 104      -2.265  63.795  36.610  1.00  0.00              
ATOM    168  O   TRP A 104      -2.057  64.664  37.458  1.00  0.00              
ATOM    169  N   ARG A 105      -3.372  63.046  36.580  1.00  0.00              
ATOM    170  CA  ARG A 105      -4.433  63.198  37.566  1.00  0.00              
ATOM    171  C   ARG A 105      -3.835  63.049  38.985  1.00  0.00              
ATOM    172  O   ARG A 105      -4.030  63.907  39.847  1.00  0.00              
ATOM    173  N   LYS A 106      -3.130  61.945  39.219  1.00  0.00              
ATOM    174  CA  LYS A 106      -2.490  61.685  40.506  1.00  0.00              
ATOM    175  C   LYS A 106      -1.663  62.891  40.932  1.00  0.00              
ATOM    176  O   LYS A 106      -1.848  63.430  42.031  1.00  0.00              
ATOM    177  N   SER A 107      -0.768  63.324  40.044  1.00  0.00              
ATOM    178  CA  SER A 107       0.109  64.426  40.341  1.00  0.00              
ATOM    179  C   SER A 107      -0.637  65.662  40.760  1.00  0.00              
ATOM    180  O   SER A 107      -0.280  66.283  41.765  1.00  0.00              
ATOM    181  N   GLN A 108      -1.665  66.028  39.998  1.00  0.00              
ATOM    182  CA  GLN A 108      -2.451  67.226  40.283  1.00  0.00              
ATOM    183  C   GLN A 108      -3.067  67.176  41.699  1.00  0.00              
ATOM    184  O   GLN A 108      -3.164  68.206  42.393  1.00  0.00              
ATOM    185  N   LYS A 109      -3.424  65.973  42.141  1.00  0.00              
ATOM    186  CA  LYS A 109      -4.037  65.811  43.440  1.00  0.00              
ATOM    187  C   LYS A 109      -3.090  66.118  44.592  1.00  0.00              
ATOM    188  O   LYS A 109      -3.518  66.550  45.671  1.00  0.00              
ATOM    189  N   GLU A 110      -1.792  66.017  44.321  1.00  0.00              
ATOM    190  CA  GLU A 110      -0.775  66.321  45.322  1.00  0.00              
ATOM    191  C   GLU A 110      -0.872  67.774  45.753  1.00  0.00              
ATOM    192  O   GLU A 110      -0.316  68.140  46.773  1.00  0.00              
ATOM    193  N   GLU A 111      -1.559  68.600  44.966  1.00  0.00              
ATOM    194  CA  GLU A 111      -1.692  70.021  45.267  1.00  0.00              
ATOM    195  C   GLU A 111      -2.876  70.383  46.155  1.00  0.00              
ATOM    196  O   GLU A 111      -3.120  71.571  46.372  1.00  0.00              
END
