Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

doi:10.1002/prot.21739

IMECH-IR > 力学所知识产出(1956-2008)

	Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters
	Liu X(刘鑫); Zhao YP(赵亚溥); Zheng WM(郑伟谋); Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China.
发表期刊	Proteins-Structure Function And Bioinformatics
	2008
页码	728-736
ISSN	0887-3585
摘要	CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.
关键词	Protein Structure
学科领域	生物力学
DOI	10.1002/prot.21739
收录类别	SCI
语种	英语
WOS记录号	WOS:000254263400019
关键词[WOS]	SUBSTITUTION MATRIX ; ALGORITHM ; DATABASE ; CLASSIFICATION ; SIMILARITIES ; BACKBONE ; FAMILIES
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
WOS类目	Biochemistry & Molecular Biology ; Biophysics
引用统计	被引频次：10[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://dspace.imech.ac.cn/handle/311007/26100
专题	力学所知识产出(1956-2008)
通讯作者	Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China.
推荐引用方式 GB/T 7714	Liu X,Zhao YP,Zheng WM,et al. Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters[J]. Proteins-Structure Function And Bioinformatics,2008:728-736.
APA	刘鑫,赵亚溥,郑伟谋,&Zheng, WM .(2008).Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters.Proteins-Structure Function And Bioinformatics,728-736.
MLA	刘鑫,et al."Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters".Proteins-Structure Function And Bioinformatics (2008):728-736.

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