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Combining local‐structure, fold‐recognition, and new fold methods for protein structure prediction
Author(s) -
Karplus Kevin,
Karchin Rachel,
Draper Jenny,
Casper Jonathan,
MandelGutfreund Yael,
Diekhans Mark,
Hughey Richard
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10540
Subject(s) - hidden markov model , protein structure prediction , fold (higher order function) , fragment (logic) , protein data bank (rcsb pdb) , computer science , alphabet , artificial intelligence , protein structure , pattern recognition (psychology) , computational biology , biology , algorithm , biochemistry , programming language , linguistics , philosophy
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. Proteins 2003;53:491–496. © 2003 Wiley‐Liss, Inc.