 
PFRMAT AL 
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 
PARENT 1fgj_A 
E 26 E 122 
E 27 E 123 
V 28 V 124 
K 29 E 125 
D 30 N 126 
E 31 N 127 
L 32 L 128 
Q 33 R 129 
K 34 S 130 
M 35 M 131 
TER 
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