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Liu, Xin; Zhao, Ya-Pu; Zheng, Wei-Mou; Zheng, WM , Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China
CLEMAPS: Multiple alignment of protein structures based on conformational letters
Source PublicationPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
KeywordSubstitution Matrix Algorithm Database Classification Similarities Backbone Families
AbstractCLEMAPS 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.
2008
ISSN0887-3585
Volume71Issue:2Pages:728-736
Subject AreaPhysics
Indexed BySCI
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Cited Times:8[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/5539
Collection理论物理所科研产出_SCI论文
Corresponding AuthorZheng, WM , Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China
Recommended Citation
GB/T 7714
Liu, Xin,Zhao, Ya-Pu,Zheng, Wei-Mou,et al. CLEMAPS: Multiple alignment of protein structures based on conformational letters[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2008,71(2):728-736.
APA Liu, Xin,Zhao, Ya-Pu,Zheng, Wei-Mou,&Zheng, WM , Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China.(2008).CLEMAPS: Multiple alignment of protein structures based on conformational letters.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,71(2),728-736.
MLA Liu, Xin,et al."CLEMAPS: Multiple alignment of protein structures based on conformational letters".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 71.2(2008):728-736.
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