Combining local-structure, fold-recognition, and new fold methods for protein structure prediction

被引：198

作者：

Karplus, K ^{[1
]}

Karchin, R ^{[1
]}

Draper, J ^{[1
]}

Casper, J ^{[1
]}

Mandel-Gutfreund, Y ^{[1
]}

Diekhans, M ^{[1
]}

Hughey, R ^{[1
]}

机构：

[1] Univ Calif Santa Cruz, Dept Comp Engn, Santa Cruz, CA 95064 USA

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2003年 / 53卷

关键词：

SAM-T02; UNDERTAKER; fragment-packing program; hidden Markov model; secondary structure;

D O I：

10.1002/prot.10540

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

This article presents an overview of the SAM-T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM-T02 server is an automatic method that uses two-track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two-track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment-packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold-recognition alignments from the SAM-T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139. (C) 2003 Wiley-Liss, Inc.

引用

页码：491 / 496

页数：6

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