High accuracy template based modeling by global optimization

被引:57
作者
Joo, Keehyoung
Lee, Jinwoo [1 ]
Lee, Sunjoong
Seo, Joo-Hyun
Lee, Sung Jong
Lee, Jooyoung
机构
[1] Sch Computat Sci, Korea Inst Adv Study, Seoul, South Korea
[2] Hanyang Univ, Dept Phys, Ansan, South Korea
[3] Seoul Natl Univ, Sch Chem & Biol Engn, Seoul, South Korea
[4] Univ Suwon, Dept Phys, Suwon, South Korea
关键词
TBM/HA; template-based modeling; protein structure prediction; global optimization; multiple alignment; side-chain modeling; model evaluation; fold recognition;
D O I
10.1002/prot.21628
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
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.
引用
收藏
页码:83 / 89
页数:7
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