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      1  CA  THR     2     115.162 -67.900  60.921  1.00  0.00              
ATOM      2  CA  ASP     3     116.546 -65.688  63.723  1.00  0.00              
ATOM      3  CA  ASP     4     117.572 -62.944  61.256  1.00  0.00              
ATOM      4  CA  SER     5     119.881 -61.166  63.699  1.00  0.00              
ATOM      5  CA  PRO     6     120.377 -58.814  60.778  1.00  0.00              
ATOM      6  CA  TYR     7     117.339 -56.687  61.485  1.00  0.00              
ATOM      7  CA  LYS     8     118.955 -55.511  64.692  1.00  0.00              
ATOM      8  CA  GLN     9     122.106 -54.801  62.787  1.00  0.00              
ATOM      9  CA  ALA    10     120.140 -52.552  60.443  1.00  0.00              
ATOM     10  CA  PHE    11     118.456 -50.829  63.389  1.00  0.00              
ATOM     11  CA  SER    12     121.529 -48.874  64.224  1.00  0.00              
ATOM     12  CA  LEU    13     122.063 -47.909  60.640  1.00  0.00              
ATOM     13  CA  PHE    14     119.189 -45.472  60.987  1.00  0.00              
ATOM     14  CA  ASP    15     120.116 -44.597  64.531  1.00  0.00              
ATOM     15  CA  ARG    16     121.536 -41.159  63.886  1.00  0.00              
ATOM     16  CA  HIS    17     122.028 -39.913  67.314  1.00  0.00              
ATOM     17  CA  GLY    18     123.862 -43.145  68.045  1.00  0.00              
ATOM     18  CA  THR    19     121.500 -43.841  70.913  1.00  0.00              
ATOM     19  CA  GLY    20     120.107 -47.080  69.459  1.00  0.00              
ATOM     20  CA  ARG    21     116.540 -46.024  70.124  1.00  0.00              
ATOM     21  CA  ILE    22     114.414 -45.036  67.090  1.00  0.00              
ATOM     22  CA  PRO    23     111.616 -42.449  66.593  1.00  0.00              
ATOM     23  CA  LYS    24     107.941 -43.371  66.142  1.00  0.00              
ATOM     24  CA  THR    25     107.733 -41.653  62.793  1.00  0.00              
ATOM     25  CA  SER    26     110.946 -43.330  61.782  1.00  0.00              
ATOM     26  CA  ILE    27     109.029 -46.540  62.375  1.00  0.00              
ATOM     27  CA  GLY    28     106.911 -46.373  59.281  1.00  0.00              
ATOM     28  CA  ASP    29     109.977 -46.111  57.111  1.00  0.00              
ATOM     29  CA  LEU    30     112.291 -48.815  58.397  1.00  0.00              
ATOM     30  CA  LEU    31     109.562 -51.366  58.226  1.00  0.00              
ATOM     31  CA  ARG    32     109.620 -50.742  54.466  1.00  0.00              
ATOM     32  CA  ALA    33     113.228 -51.667  53.761  1.00  0.00              
ATOM     33  CA  CYS    34     112.771 -54.766  55.916  1.00  0.00              
ATOM     34  CA  GLY    35     111.242 -57.156  53.372  1.00  0.00              
ATOM     35  CA  GLN    36     107.684 -55.811  53.150  1.00  0.00              
ATOM     36  CA  ASN    37     105.707 -52.900  51.793  1.00  0.00              
ATOM     37  CA  PRO    38     103.136 -51.782  54.429  1.00  0.00              
ATOM     38  CA  THR    39     100.748 -48.850  53.827  1.00  0.00              
ATOM     39  CA  LEU    40     100.128 -45.509  55.540  1.00  0.00              
ATOM     40  CA  ALA    41      96.849 -45.556  57.363  1.00  0.00              
ATOM     41  CA  GLU    42      97.826 -49.116  58.116  1.00  0.00              
ATOM     42  CA  ILE    43     100.836 -48.113  60.158  1.00  0.00              
ATOM     43  CA  THR    44      98.953 -45.208  61.601  1.00  0.00              
ATOM     44  CA  GLU    45      96.287 -47.654  62.792  1.00  0.00              
ATOM     45  CA  ILE    46      99.270 -48.863  64.876  1.00  0.00              
ATOM     46  CA  GLU    47     101.187 -47.037  67.614  1.00  0.00              
ATOM     47  CA  VAL    54     111.372 -46.800  71.373  1.00  0.00              
ATOM     48  CA  ASP    55     113.924 -49.608  70.739  1.00  0.00              
ATOM     49  CA  MET    56     114.393 -53.121  69.113  1.00  0.00              
ATOM     50  CA  GLU    57     111.878 -53.710  71.840  1.00  0.00              
ATOM     51  CA  GLN    58     108.780 -52.619  69.982  1.00  0.00              
ATOM     52  CA  PHE    59     110.278 -52.540  66.521  1.00  0.00              
ATOM     53  CA  LEU    60     110.650 -56.304  66.132  1.00  0.00              
ATOM     54  CA  GLN    61     107.094 -56.827  67.341  1.00  0.00              
ATOM     55  CA  VAL    62     105.558 -53.902  65.493  1.00  0.00              
ATOM     56  CA  LEU    63     107.445 -55.177  62.498  1.00  0.00              
ATOM     57  CA  ASN    64     106.432 -58.830  62.522  1.00  0.00              
ATOM     58  CA  ARG    65     102.943 -57.480  62.689  1.00  0.00              
ATOM     59  CA  PRO    66     103.125 -56.101  59.149  1.00  0.00              
ATOM     60  CA  ASN    67     104.831 -59.239  58.000  1.00  0.00              
ATOM     61  CA  GLY    68     101.540 -60.654  58.459  1.00  0.00              
ATOM     62  CA  PHE    69      99.152 -58.996  56.011  1.00  0.00              
ATOM     63  CA  ASP    70     102.032 -58.737  53.604  1.00  0.00              
ATOM     64  CA  MET    71     100.410 -61.280  51.249  1.00  0.00              
END 
