| SANA: an algorithm for sequential and non-sequential protein structure alignment. | |
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MedLine Citation:
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PMID: 20127263 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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Lin Wang; Ling-Yun Wu; Yong Wang; Xiang-Sun Zhang; Luonan Chen |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-02-02 |
Journal Detail:
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Title: Amino acids Volume: 39 ISSN: 1438-2199 ISO Abbreviation: Amino Acids Publication Date: 2010 Jul |
Date Detail:
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Created Date: 2010-06-25 Completed Date: 2010-10-04 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9200312 Medline TA: Amino Acids Country: Austria |
Other Details:
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Languages: eng Pagination: 417-25 Citation Subset: IM |
Affiliation:
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Computer Science and Information Engineering College, Tianjin University of Science and Technology, Tianjin, 300222, China. juanzi_1982_49@126.com |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms* Computational Biology / methods* Databases, Protein Models, Molecular Sequence Alignment / methods* Software |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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