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High accuracy template based modeling by global optimization
Author(s) -
Joo Keehyoung,
Lee Jinwoo,
Lee Sunjoong,
Seo JooHyun,
Lee Sung Jong,
Lee Jooyoung
Publication year - 2007
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.21628
Subject(s) - modeller , template , computer science , simulated annealing , consistency (knowledge bases) , protein structure prediction , a priori and a posteriori , function (biology) , global optimization , chain (unit) , algorithm , artificial intelligence , homology modeling , protein structure , physics , philosophy , enzyme , epistemology , astronomy , evolutionary biology , biology , programming language , nuclear magnetic resonance
For high‐accuracy template‐based‐modeling of CASP7 targets, we have applied a procedure based on the rigorous optimization of score functions at three stages: multiple alignment, chain building, and side‐chain modeling. We applied the conformational space annealing method to a newly developed consistency based score function for multiple alignment. For chain building, we optimized the MODELLER energy function. For side‐chain modeling, we optimized a SCWRL‐like energy function using a rotamer library constructed specifically for a given target sequence. By rigorous optimization, we have achieved significant improvement in backbone as well as side‐chain modeling for TBM and TBM/HA targets. For most TBM/HA targets (17/26), the predicted model was more accurate than the model one can construct from the best template in a posteriori fashion. It appears that the current method can extract relevant information out of multiple templates. Proteins 2007. © 2007 Wiley‐Liss, Inc.
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