Incorporating Ab Initio energy into threading approaches for protein structure prediction

doi:10.1186/1471-2105-12-S1-S54

	Incorporating Ab Initio energy into threading approaches for protein structure prediction
	Shao, MF ; Wang, S ; Wang, C 1; Yuan, XY ; Li, SC ; Zheng, WM ; Bu, DB
	2011
会议日期	JAN 11-14, 2011
会议地点	Incheon, SOUTH KOREA
关键词	FOLD RECOGNITION ALIGNMENT GENERATION SEQUENCES FRAGMENTS PROFILES
卷号	12
DOI	10.1186/1471-2105-12-S1-S54
页码	S54
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.
会议录	BMC BIOINFORMATICS
会议录出版者	BIOMED CENTRAL LTD
会议录出版地	LONDON
语种	英语
URL标识	查看原文
ISSN号	1471-2105
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
内容类型	会议论文
源URL	[http://ir.itp.ac.cn/handle/311006/23620]
专题	SCI会议论文
作者单位	1.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China 2.Int Comp Sci Inst, Berkeley, CA 94704 USA 3.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Shao, MF,Wang, S,Wang, C,et al. Incorporating Ab Initio energy into threading approaches for protein structure prediction[C]. 见:. Incheon, SOUTH KOREA. JAN 11-14, 2011.