REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0084AL019_1_3 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0084  
AUTHOR 9070-5088-8627  
REMARK   
REMARK Prediction date: 2 Sept 1998  
REMARK Group name: UCSC-compbio  
REMARK Students: Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate,  
REMARK Faculty:  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   
METHOD Since this peptide was supposed to be a de novo design, we did not  
METHOD expect evolutionary information from similar sequences in the protein  
METHOD data base, but we searched anyway.  We found two proteins with pieces  
METHOD that matched the peptide: one from desmoplakin I [Homo sapiens] and  
METHOD one from ependymin [4 different species].  
METHOD   
METHOD gi|2134996|pir||A38194	tvcldLDKVEAYRCGLKKIKNDLNLKKSLLATMKTELQKAQQihsqt. 607:643   
METHOD 			         E     L    N L   KSLL   K ELQK  Q  
METHOD T0084			.....CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ...... 1:37  
METHOD 			             KKLR VENE H NK     V  
METHOD gi|998296		diaegXFNYDSTAKKLRFVENESHANKTSHMDVLIHFEEGVLyeids. 20:56  
METHOD gi|998286 		diavgDFNYDSTAKKLRFVENESHANKTSHMDVLIHFEEGVLyemds. 31:67  
METHOD gi|998304 		diadgEFNYDSTAKKLRFVENESHSNKTSHMDVLIHFEEGVLyeids. 29:65  
METHOD gi|998302 		diaegEFNYDSTAKKLRFVENESHSNKTSHMDVLIHFEEGVLyeids. 27:63  
METHOD   
METHOD Unfortunately, neither of these proteins have known structures, though  
METHOD the desmoplakin I match is to part of a 2-strand coiled-coil domain.  
METHOD   
METHOD We did not find a full-length match for this peptide in PDB, but we  
METHOD did find several partial matches.  Based on these partial matches,   
METHOD we can piece together the prediction from three pieces   
METHOD          
METHOD 4blmA	IGGPESLKKELRKI  
METHOD 4blmA	LLLHHHHHHHHHHL  
METHOD          GG E   K LR  
METHOD   
METHOD 1ft1A	   RQWVIQEFRLWDNELQYVDQLLKE  
METHOD 1ft1A	   HHHHHHHLLLLLLHHHHHHHHHHH  
METHOD 	   R  V    R   NEL Y   LL E  
METHOD   
METHOD 1fgjA	              DDPLYYKKGKLEEVENNLRSM  
METHOD 1fgjA	              LLGGGHHHHHHHHHHHHHHHL  
METHOD 	                 L Y K  LEEV   L  M  
METHOD   
METHOD   
METHOD and predict the following secondary structure:  
METHOD 	  
METHOD 	CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ  
METHOD 	LLLHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHLLL  
METHOD   
METHOD Since we do not have the tools here to put these fragments into a  
METHOD single coordinate system, we are just submitting them as separate  
METHOD pieces.  
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1fgj_A 
ATOM      1  N   GLU    26      23.227   8.300  32.300  1.00  0.00              
ATOM      2  CA  GLU    26      22.290   7.266  31.859  1.00  0.00              
ATOM      3  C   GLU    26      21.634   6.618  33.062  1.00  0.00              
ATOM      4  O   GLU    26      20.416   6.417  33.101  1.00  0.00              
ATOM      5  N   GLU    27      22.472   6.275  34.031  1.00  0.00              
ATOM      6  CA  GLU    27      22.053   5.646  35.275  1.00  0.00              
ATOM      7  C   GLU    27      20.965   6.482  35.947  1.00  0.00              
ATOM      8  O   GLU    27      19.863   5.985  36.198  1.00  0.00              
ATOM      9  N   VAL    28      21.263   7.763  36.167  1.00  0.00              
ATOM     10  CA  VAL    28      20.328   8.713  36.780  1.00  0.00              
ATOM     11  C   VAL    28      18.979   8.679  36.067  1.00  0.00              
ATOM     12  O   VAL    28      17.928   8.596  36.703  1.00  0.00              
ATOM     13  N   LYS    29      19.019   8.756  34.742  1.00  0.00              
ATOM     14  CA  LYS    29      17.810   8.749  33.939  1.00  0.00              
ATOM     15  C   LYS    29      16.992   7.501  34.181  1.00  0.00              
ATOM     16  O   LYS    29      15.764   7.564  34.213  1.00  0.00              
ATOM     17  N   ASP    30      17.670   6.377  34.402  1.00  0.00              
ATOM     18  CA  ASP    30      16.980   5.117  34.669  1.00  0.00              
ATOM     19  C   ASP    30      16.385   5.100  36.073  1.00  0.00              
ATOM     20  O   ASP    30      15.360   4.454  36.315  1.00  0.00              
ATOM     21  N   GLU    31      17.037   5.796  37.002  1.00  0.00              
ATOM     22  CA  GLU    31      16.539   5.879  38.367  1.00  0.00              
ATOM     23  C   GLU    31      15.213   6.615  38.321  1.00  0.00              
ATOM     24  O   GLU    31      14.222   6.159  38.901  1.00  0.00              
ATOM     25  N   LEU    32      15.189   7.721  37.580  1.00  0.00              
ATOM     26  CA  LEU    32      13.996   8.546  37.443  1.00  0.00              
ATOM     27  C   LEU    32      12.832   7.843  36.736  1.00  0.00              
ATOM     28  O   LEU    32      11.672   8.052  37.094  1.00  0.00              
ATOM     29  N   GLN    33      13.136   7.049  35.711  1.00  0.00              
ATOM     30  CA  GLN    33      12.105   6.311  34.982  1.00  0.00              
ATOM     31  C   GLN    33      11.427   5.344  35.951  1.00  0.00              
ATOM     32  O   GLN    33      10.197   5.318  36.064  1.00  0.00              
ATOM     33  N   LYS    34      12.246   4.584  36.676  1.00  0.00              
ATOM     34  CA  LYS    34      11.769   3.617  37.661  1.00  0.00              
ATOM     35  C   LYS    34      10.867   4.308  38.689  1.00  0.00              
ATOM     36  O   LYS    34       9.887   3.724  39.150  1.00  0.00              
ATOM     37  N   MET    35      11.185   5.557  39.029  1.00  0.00              
ATOM     38  CA  MET    35      10.399   6.317  40.001  1.00  0.00              
ATOM     39  C   MET    35       9.309   7.142  39.365  1.00  0.00              
ATOM     40  O   MET    35       8.673   7.960  40.031  1.00  0.00              
END
