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SANA: an algorithm for sequential and non-sequential protein structure alignment
Wang, Lin1,2; Wu, Ling-Yun1; Wang, Yong1; Zhang, Xiang-Sun1; Chen, Luonan3
Source PublicationAMINO ACIDS
AbstractProtein 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.
KeywordProtein structure alignment Fold comparison Circular permutation Functional sites
Funding ProjectNational 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 Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemistry & Molecular Biology
WOS IDWOS:000279190400011
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Document Type期刊论文
Corresponding AuthorZhang, Xiang-Sun
Affiliation1.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
Recommended Citation
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.
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