Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation

被引：56

作者：

Cao, Yang ^{[1
,2
]}

Song, Lin ^{[1
,2
]}

Miao, Zhichao ^{[1
,2
]}

Hu, Yun ^{[1
,2
]}

Tian, Liqing ^{[1
,2
]}

Jiang, Taijiao ^{[1
]}

机构：

[1] Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China

[2] Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China

来源：

BIOINFORMATICS | 2011年 / 27卷 / 06期

关键词：

DEAD-END ELIMINATION; ENERGY FUNCTION; PREDICTION; PROTEINS; CONFORMATIONS; LIBRARY; ALGORITHM; ACCURACY; PACKING; SURFACES;

D O I：

10.1093/bioinformatics/btr009

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy. Results: We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.

引用

页码：785 / 790

页数：6

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