A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

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	A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features
	Liu X(刘鑫); Zhao YP(赵亚溥); Liu X(刘鑫); Zhao YP(赵亚溥); Zhao YP(赵亚溥)
刊名	Journal of Theoretical Biology
	2009
通讯作者邮箱	yzhao@imech.ac.cn
卷号	261 期号:4 页码:593-597
关键词	Scoring scheme Hydrophobic interaction Multiple sequence alignment Homologous proteins
ISSN号	0022-5193
通讯作者	赵亚溥
合作状况	其它
中文摘要	As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.
学科主题	固体力学
关键词[WOS]	ACID SUBSTITUTION MATRICES; PROTEIN; COMPLEXITY; REDUCTION; ALPHABET; DATABASE; MODELS
收录类别	SCI
语种	英语
WOS记录号	WOS:000274799100009
公开日期	2009-12-28
内容类型	期刊论文
源URL	[http://dspace.imech.ac.cn/handle/311007/28813]
专题	力学研究所_非线性力学国家重点实验室
通讯作者	Zhao YP(赵亚溥)
推荐引用方式 GB/T 7714	Liu X,Zhao YP,Liu X,et al. A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features[J]. Journal of Theoretical Biology,2009,261(4):593-597.
APA	Liu X,Zhao YP,Liu X,Zhao YP,&赵亚溥.(2009).A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features.Journal of Theoretical Biology,261(4),593-597.
MLA	Liu X,et al."A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features".Journal of Theoretical Biology 261.4(2009):593-597.