REMARK  ----------------------------------------------------------  
REMARK  Molecule : T0076AL019_1  
REMARK  Alignment model prepared for CASP3 experiment  
REMARK  by group : UCSC-COMPBIO  
REMARK  ----------------------------------------------------------  
TARGET T0076   
AUTHOR 9070-5088-8627   
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    
METHOD T0076 clearly has 2 EF-hand domains, with very high similarity to   
METHOD calmodulins (such as 1deg).   
METHOD    
METHOD Because the problem is to distinguish which of the many EF-hand   
METHOD domains is the closest model, we chose to use only the second   
METHOD iteration of the target-alignment-building process for our target HMM.   
METHOD    
METHOD The calmodulins provide a good fit to the EF-hand domains, but the   
METHOD central helix would be disrupted by the prolines and glycines in   
METHOD PNGFDMPGDP.   Myosins are a much better fit for the central helix,   
METHOD particularly 2mysC.  Unfortunately, 2mysC has a chain-tracing error in   
METHOD the first domain, so is a bit dangerous to use as a basis for homology   
METHOD modeling.   
METHOD    
METHOD We finally decided to use 1almC, a theoretical model based on 2mysC,   
METHOD which seems to fix the chain-tracing error. We unaligned the second   
METHOD binding-pocket of the first EF-hand, since it is much shorter in   
METHOD T0076, and 1almC seems to be untrustworthy in that loop.  None of the   
METHOD other calmodulin-like domains we looked at had a loop that we could   
METHOD confidently plug in to fill the gap, so we just left it unaligned.   
MODEL 1   
REMARK  ----------------------------------------------------------  
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov  
REMARK  ----------------------------------------------------------  
REMARK  Coordinates assigned from PDB entry: 1alm_C  
ATOM     65  CA  PRO    72      99.029 -58.392  49.211  1.00  0.00              
ATOM     66  CA  GLY    73     102.533 -58.210  47.727  1.00  0.00              
ATOM     67  CA  ASP    74     100.478 -59.995  45.085  1.00  0.00              
ATOM     68  CA  PRO    75     101.418 -58.782  41.670  1.00  0.00              
ATOM     69  CA  GLU    76      98.498 -60.273  39.694  1.00  0.00              
ATOM     70  CA  GLU    77      96.638 -57.062  40.367  1.00  0.00              
ATOM     71  CA  PHE    78      99.251 -54.420  39.697  1.00  0.00              
ATOM     72  CA  VAL    79     100.254 -54.485  36.086  1.00  0.00              
ATOM     73  CA  LYS    80      96.541 -54.658  35.500  1.00  0.00              
ATOM     74  CA  GLY    81      95.383 -51.474  37.248  1.00  0.00              
ATOM     75  CA  PHE    82      97.686 -49.377  35.230  1.00  0.00              
ATOM     76  CA  GLN    83      96.283 -50.657  31.845  1.00  0.00              
ATOM     77  CA  VAL    84      93.095 -49.179  33.152  1.00  0.00              
ATOM     78  CA  PHE    85      94.595 -45.735  33.140  1.00  0.00              
ATOM     79  CA  ASP    86      95.623 -45.786  29.540  1.00  0.00              
ATOM     80  CA  LYS    87      95.344 -48.778  27.322  1.00  0.00              
ATOM     81  CA  ASP    88      95.017 -48.198  23.607  1.00  0.00              
ATOM     82  CA  ALA    89      97.062 -51.140  22.447  1.00  0.00              
ATOM     83  CA  THR    90     100.223 -51.409  24.421  1.00  0.00              
ATOM     84  CA  GLY    91     100.787 -51.133  28.150  1.00  0.00              
ATOM     85  CA  MET    92     100.533 -47.431  27.433  1.00  0.00              
ATOM     86  CA  ILE    93     100.227 -44.718  30.065  1.00  0.00              
ATOM     87  CA  GLY    94     101.168 -41.062  29.708  1.00  0.00              
ATOM     88  CA  VAL    95     103.460 -39.300  32.134  1.00  0.00              
ATOM     89  CA  GLY    96     101.041 -36.680  33.340  1.00  0.00              
ATOM     90  CA  GLU    97      98.368 -39.191  34.241  1.00  0.00              
ATOM     91  CA  LEU    98     100.520 -41.237  36.559  1.00  0.00              
ATOM     92  CA  ARG    99     102.388 -38.228  37.862  1.00  0.00              
ATOM     93  CA  TYR   100      99.265 -36.455  39.037  1.00  0.00              
ATOM     94  CA  VAL   101      97.391 -39.599  39.968  1.00  0.00              
ATOM     95  CA  LEU   102     100.198 -40.613  42.326  1.00  0.00              
ATOM     96  CA  THR   103     100.604 -37.200  43.963  1.00  0.00              
ATOM     97  CA  SER   104      96.934 -36.337  44.564  1.00  0.00              
ATOM     98  CA  LEU   105      94.765 -39.394  44.951  1.00  0.00              
ATOM     99  CA  GLY   106      94.646 -41.669  47.926  1.00  0.00              
ATOM    100  CA  GLU   107      97.769 -41.503  49.995  1.00  0.00              
ATOM    101  CA  LYS   108      99.329 -38.723  47.983  1.00  0.00              
ATOM    102  CA  LEU   109     103.051 -39.068  47.408  1.00  0.00              
ATOM    103  CA  SER   110     105.426 -36.177  46.799  1.00  0.00              
ATOM    104  CA  ASN   111     106.274 -34.339  43.576  1.00  0.00              
ATOM    105  CA  GLU   112     109.852 -34.936  44.609  1.00  0.00              
ATOM    106  CA  GLU   113     109.286 -38.635  45.222  1.00  0.00              
ATOM    107  CA  MET   114     107.304 -39.345  42.136  1.00  0.00              
ATOM    108  CA  ASP   115     109.705 -37.483  39.948  1.00  0.00              
ATOM    109  CA  GLU   116     112.183 -39.930  41.331  1.00  0.00              
ATOM    110  CA  LEU   117     110.021 -42.911  40.576  1.00  0.00              
ATOM    111  CA  LEU   118     109.817 -41.547  37.050  1.00  0.00              
ATOM    112  CA  LYS   119     113.518 -42.038  36.691  1.00  0.00              
ATOM    113  CA  GLY   120     114.622 -42.140  33.063  1.00  0.00              
ATOM    114  CA  VAL   121     112.150 -44.920  32.379  1.00  0.00              
ATOM    115  CA  PRO   122     109.769 -42.370  30.838  1.00  0.00              
ATOM    116  CA  VAL   123     111.364 -40.839  27.801  1.00  0.00              
ATOM    117  CA  LYS   124     110.353 -38.004  25.521  1.00  0.00              
ATOM    118  CA  ASP   125     108.063 -40.621  24.047  1.00  0.00              
ATOM    119  CA  GLY   126     105.704 -38.884  26.478  1.00  0.00              
ATOM    120  CA  MET   127     104.098 -42.243  27.002  1.00  0.00              
ATOM    121  CA  VAL   128     105.233 -44.787  29.529  1.00  0.00              
ATOM    122  CA  ASN   129     105.302 -48.553  29.210  1.00  0.00              
ATOM    123  CA  TYR   130     103.581 -49.909  32.245  1.00  0.00              
ATOM    124  CA  HIS   131     104.628 -53.502  31.897  1.00  0.00              
ATOM    125  CA  ASP   132     108.142 -52.677  32.975  1.00  0.00              
ATOM    126  CA  PHE   133     107.301 -50.047  35.349  1.00  0.00              
ATOM    127  CA  VAL   134     106.009 -52.593  37.805  1.00  0.00              
ATOM    128  CA  GLN   135     108.918 -54.906  37.127  1.00  0.00              
ATOM    129  CA  MET   136     111.342 -52.106  37.908  1.00  0.00              
ATOM    130  CA  ILE   137     109.246 -51.149  40.948  1.00  0.00              
ATOM    131  CA  LEU   138     108.877 -54.715  42.212  1.00  0.00              
ATOM    132  CA  ALA   139     112.646 -54.763  41.866  1.00  0.00              
ATOM    133  CA  ASN   140     114.204 -53.473  45.065  1.00  0.00              
END 
