The use of a conformational alphabet for fast alignment of protein structures

	The use of a conformational alphabet for fast alignment of protein structures
	Zheng, WM
	2008
会议日期	MAY 06-09, 2008
会议地点	Georgia State Univ, Atlanta, GA
关键词	SUBSTITUTION MATRIX ALGORITHM CE
卷号	4983
页码	331-342
英文摘要	A protein conformational alphabet refers to the discretized states of the three-dimensional segmental structure of protein backbones. Here a letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues, and our alphabet consist of 17 letters obtained by clustering based on the probability distribution of these angles. A substitution matrix called CLESUM has been derived from an alignment database of representative structures to measure both evolutionary and geometrical similarity between any two such letters. A structural fragment is then mapped to a string, and two strings with their CLESUM score being higher than a preset threshold form a similar fragment pair (SFP). The search for SFPs by string comparison is fast. Furthermore, CLESUM scores reflect the importance of SFPs to structure alignment, and then the search space can be significantly-reduced. A fast tool for pairwise alignment called CLePAPS is developed by collecting as many spatially consistent SFPs a's possible. Extending the concept of SFPs to that of similar fragment blocks for multiple structure alignment leads to a fast tool for multiple structure alignment called BLOMAPS. Both CLePAPS and BLOMAPS are tested on ensembles of various structures. They are reliable, and about two or three orders faster than some well-known algorithms.
源文献作者	Georgia State Univ
会议录	BIOINFORMATICS RESEARCH AND APPLICATIONS
会议录出版者	SPRINGER-VERLAG BERLIN
会议录出版地	BERLIN
语种	英语
ISSN号	0302-9743
ISBN号	978-3-540-79449-3
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Mathematical & Computational Biology
内容类型	会议论文
源URL	[http://ir.itp.ac.cn/handle/311006/23661]
专题	SCI会议论文
作者单位	Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Zheng, WM. The use of a conformational alphabet for fast alignment of protein structures[C]. 见:. Georgia State Univ, Atlanta, GA. MAY 06-09, 2008.