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题名: CLEMAPS: Multiple alignment of protein structures based on conformational letters
作者: Liu, Xin ;  Zhao, Ya-Pu ;  Zheng, Wei-Mou
刊名: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
出版日期: 2008
卷号: 71, 期号:2, 页码:728-736
关键词: SUBSTITUTION MATRIX ;  ALGORITHM ;  DATABASE ;  CLASSIFICATION ;  SIMILARITIES ;  BACKBONE ;  FAMILIES
学科分类: Physics
通讯作者: Zheng, WM , Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China
部门归属: [Liu, X; Zhao, YP] Chinese Acad Sci, Inst Mech, Beijing 100080, Peoples R China; [Zheng, WM] Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
英文摘要: 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.
收录类别: SCI
原文出处: 查看原文
WOS记录号: WOS:000254263400019
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/5539
Appears in Collections:理论物理所1978-2010年知识产出_期刊论文

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Recommended Citation:
Liu, Xin,Zhao, Ya-Pu,Zheng, Wei-Mou. CLEMAPS: Multiple alignment of protein structures based on conformational letters[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2008,71(2):728-736.
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