REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0084AL019_1_2 
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: 1ft1_A 
ATOM      1  N   ARG    12      62.596  91.066  39.502  1.00  0.00              
ATOM      2  CA  ARG    12      64.054  90.999  39.418  1.00  0.00              
ATOM      3  C   ARG    12      64.744  92.166  40.125  1.00  0.00              
ATOM      4  O   ARG    12      65.575  92.839  39.529  1.00  0.00              
ATOM      5  N   ALA    13      64.432  92.403  41.395  1.00  0.00              
ATOM      6  CA  ALA    13      65.051  93.517  42.129  1.00  0.00              
ATOM      7  C   ALA    13      66.223  93.072  43.019  1.00  0.00              
ATOM      8  O   ALA    13      66.250  93.372  44.216  1.00  0.00              
ATOM      9  N   VAL    14      67.233  92.452  42.409  1.00  0.00              
ATOM     10  CA  VAL    14      68.412  91.937  43.118  1.00  0.00              
ATOM     11  C   VAL    14      69.530  92.918  43.428  1.00  0.00              
ATOM     12  O   VAL    14      70.366  92.668  44.297  1.00  0.00              
ATOM     13  N   GLU    15      69.553  94.025  42.704  1.00  0.00              
ATOM     14  CA  GLU    15      70.601  95.027  42.839  1.00  0.00              
ATOM     15  C   GLU    15      71.107  95.404  44.212  1.00  0.00              
ATOM     16  O   GLU    15      72.312  95.396  44.439  1.00  0.00              
ATOM     17  N   ASN    16      70.202  95.714  45.131  1.00  0.00              
ATOM     18  CA  ASN    16      70.627  96.160  46.456  1.00  0.00              
ATOM     19  C   ASN    16      70.303  95.286  47.647  1.00  0.00              
ATOM     20  O   ASN    16      70.485  95.712  48.788  1.00  0.00              
ATOM     21  N   GLU    17      69.863  94.059  47.407  1.00  0.00              
ATOM     22  CA  GLU    17      69.509  93.208  48.521  1.00  0.00              
ATOM     23  C   GLU    17      70.702  92.780  49.352  1.00  0.00              
ATOM     24  O   GLU    17      70.631  92.809  50.578  1.00  0.00              
ATOM     25  N   LEU    18      71.818  92.457  48.715  1.00  0.00              
ATOM     26  CA  LEU    18      72.980  92.013  49.479  1.00  0.00              
ATOM     27  C   LEU    18      73.465  93.108  50.424  1.00  0.00              
ATOM     28  O   LEU    18      74.001  92.833  51.497  1.00  0.00              
ATOM     29  N   HIS    19      73.251  94.354  50.034  1.00  0.00              
ATOM     30  CA  HIS    19      73.652  95.464  50.866  1.00  0.00              
ATOM     31  C   HIS    19      72.673  95.525  52.032  1.00  0.00              
ATOM     32  O   HIS    19      73.083  95.702  53.180  1.00  0.00              
ATOM     33  N   TYR    20      71.385  95.339  51.742  1.00  0.00              
ATOM     34  CA  TYR    20      70.354  95.365  52.778  1.00  0.00              
ATOM     35  C   TYR    20      70.665  94.282  53.818  1.00  0.00              
ATOM     36  O   TYR    20      70.649  94.522  55.029  1.00  0.00              
ATOM     37  N   ASN    21      70.993  93.102  53.318  1.00  0.00              
ATOM     38  CA  ASN    21      71.348  91.968  54.146  1.00  0.00              
ATOM     39  C   ASN    21      72.550  92.316  55.033  1.00  0.00              
ATOM     40  O   ASN    21      72.640  91.861  56.174  1.00  0.00              
ATOM     41  N   LYS    22      73.480  93.106  54.500  1.00  0.00              
ATOM     42  CA  LYS    22      74.663  93.507  55.256  1.00  0.00              
ATOM     43  C   LYS    22      74.279  94.458  56.371  1.00  0.00              
ATOM     44  O   LYS    22      74.904  94.461  57.427  1.00  0.00              
ATOM     45  N   SER    23      73.276  95.291  56.107  1.00  0.00              
ATOM     46  CA  SER    23      72.760  96.243  57.082  1.00  0.00              
ATOM     47  C   SER    23      72.103  95.487  58.250  1.00  0.00              
ATOM     48  O   SER    23      72.484  95.659  59.414  1.00  0.00              
ATOM     49  N   LEU    24      71.121  94.645  57.935  1.00  0.00              
ATOM     50  CA  LEU    24      70.429  93.872  58.955  1.00  0.00              
ATOM     51  C   LEU    24      71.336  92.924  59.735  1.00  0.00              
ATOM     52  O   LEU    24      71.086  92.668  60.913  1.00  0.00              
ATOM     53  N   LEU    25      72.361  92.372  59.094  1.00  0.00              
ATOM     54  CA  LEU    25      73.258  91.467  59.804  1.00  0.00              
ATOM     55  C   LEU    25      74.056  92.229  60.851  1.00  0.00              
ATOM     56  O   LEU    25      74.476  91.651  61.863  1.00  0.00              
END
