Incorporating Ab Initio energy into threading approaches for protein structure prediction

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	Incorporating Ab Initio energy into threading approaches for protein structure prediction
	Zheng, WM
刊名	BMC BIOINFORMATICS
	2011
卷号	12 期号:*页码:S54
关键词	FOLD RECOGNITION ALIGNMENT GENERATION SEQUENCES FRAGMENTS PROFILES
ISSN号	1471-2105
通讯作者	Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China.
英文摘要	Background: Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches-threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates. Results: In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the "partial" decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function. Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison. Conclusions: Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy.
学科主题	Physics
收录类别	SCI
原文出处	http://dx.doi.org/10.1186/1471-2105-12-S1-S54
语种	英语
WOS记录号	WOS:000290221000055
公开日期	2013-05-17
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/14407]
专题	理论物理研究所_理论物理所1978-2010年知识产出
推荐引用方式 GB/T 7714	Zheng, WM. Incorporating Ab Initio energy into threading approaches for protein structure prediction[J]. BMC BIOINFORMATICS,2011,12(*):S54.
APA	Zheng, WM.(2011).Incorporating Ab Initio energy into threading approaches for protein structure prediction.BMC BIOINFORMATICS,12(*),S54.
MLA	Zheng, WM."Incorporating Ab Initio energy into threading approaches for protein structure prediction".BMC BIOINFORMATICS 12.*(2011):S54.