SANA: an algorithm for sequential and non-sequential protein structure alignment

doi:10.1007/s00726-009-0457-y

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	SANA: an algorithm for sequential and non-sequential protein structure alignment
	Wang, Lin 1,2; Wu, Ling-Yun1 ; Wang, Yong1 ; Zhang, Xiang-Sun1 ; Chen, Luonan 3
	2010-07-01
发表期刊	AMINO ACIDS
ISSN	0939-4451
卷号	39 期号:2 页码:417-425
摘要	Protein structure alignment algorithms play an important role in the studies of protein structure and function. In this paper, a novel approach for structure alignment is presented. Specifically, core regions in two protein structures are first aligned by identifying connected components in a network of neighboring geometrically compatible aligned fragment pairs. The initial alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential alignments. We show the superior performance of the proposed algorithm by the computational experiments on several benchmark datasets and the comparisons with the well-known structure alignment algorithms such as DALI, CE and MATT. The proposed method can obtain accurate and biologically significant alignment results for the case with occurrence of internal repeats or indels, identify the circular permutations, and reveal conserved functional sites. A ranking criterion of our algorithm for fold similarity is presented and found to be comparable or superior to the Z-score of CE in most cases from the numerical experiments. The software and supplementary data of computational results are available at http://zhangroup.aporc.org/bioinfo/SANA.
关键词	Protein structure alignment Fold comparison Circular permutation Functional sites
DOI	10.1007/s00726-009-0457-y
语种	英语
资助项目	National Natural Science Foundation of China (NSFC)[10631070] ; National Natural Science Foundation of China (NSFC)[60503004] ; JSPS-NSFC[10711140116] ; Chief Scientist Program of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences[2009CSP002]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000279190400011
出版者	SPRINGER
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/9286
专题	应用数学研究所
通讯作者	Zhang, Xiang-Sun
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Tianjin Univ Sci & Technol, Comp Sci & Informat Engn Coll, Tianjin 300222, Peoples R China 3.Chinese Acad Sci, SIBS Novo Nordisk Translat Res Ctr PreDiabet, Key Lab Syst Biol, Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China
推荐引用方式 GB/T 7714	Wang, Lin,Wu, Ling-Yun,Wang, Yong,et al. SANA: an algorithm for sequential and non-sequential protein structure alignment[J]. AMINO ACIDS,2010,39(2):417-425.
APA	Wang, Lin,Wu, Ling-Yun,Wang, Yong,Zhang, Xiang-Sun,&Chen, Luonan.(2010).SANA: an algorithm for sequential and non-sequential protein structure alignment.AMINO ACIDS,39(2),417-425.
MLA	Wang, Lin,et al."SANA: an algorithm for sequential and non-sequential protein structure alignment".AMINO ACIDS 39.2(2010):417-425.