Premium
SAM‐T04: What is new in protein–structure prediction for CASP6
Author(s) -
Karplus Kevin,
Katzman Sol,
Shackleford George,
Koeva Martina,
Draper Jenny,
Barnes Bret,
Soriano Marcia,
Hughey Richard
Publication year - 2005
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.20730
Subject(s) - protocol (science) , template , computer science , protein structure prediction , fragment (logic) , range (aeronautics) , computational biology , casp , protein structure , data mining , artificial intelligence , biology , algorithm , programming language , medicine , biochemistry , materials science , alternative medicine , pathology , composite material
The SAM‐T04 method for predicting protein structures uses a single protocol across the entire range of targets, from comparative modeling to new folds. This protocol is similar to the SAM‐T02 protocol used in CASP5, but has improvements in the iterative search for similar sequences in finding and aligning templates, in creating fragment libraries, in generating protein conformations, and in scoring the conformations. The automatic procedure made some improvements over simply selecting an alignment to the highest‐scoring template, and human intervention made substantial improvements over the automatic procedure. The main improvements made by human intervention were from adding constraints to build (or retain) β‐sheets and from splitting multidomain proteins into separate domains. The uniform protocol was moderately successful across the entire range of target difficulty, but was somewhat less successful than other approaches in CASP6 on the comparative modeling targets. Proteins 2005;Suppl 7:135–142. © 2005 Wiley‐Liss, Inc.