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Evaluating Protein Similarity from Coarse Structures
Wang, Yong1; Wu, Ling-Yun1; Zhang, Ji-Hong2; Zhan, Zhong-Wei; Zhang, Xiang-Sun1; Chen, Luonan3
2009-10-01
Source PublicationIEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN1545-5963
Volume6Issue:4Pages:583-593
AbstractTo unscramble the relationship between protein function and protein structure, it is essential to assess the protein similarity from different aspects. Although many methods have been proposed for protein structure alignment or comparison, alternative similarity measures are still strongly demanded due to the requirement of fast screening and query in large-scale structure databases. In this paper, we first formulate a novel representation of a protein structure, i.e., Feature Sequence of Surface (FSS). Then, a new score scheme is developed to measure the similarity between two representations. To verify the proposed method, numerical experiments are conducted in four different protein data sets. We also classify SARS coronavirus to verify the effectiveness of the new method. Furthermore, preliminary results of fast classification of the whole CATH v2.5.1 database based on the new macrostructure similarity are given as a pilot study. We demonstrate that the proposed approach to measure the similarities between protein structures is simple to implement, computationally efficient, and surprisingly fast. In addition, the method itself provides a new and quantitative tool to view a protein structure.
KeywordProtein structure structure comparison protein surface
DOI10.1109/TCBB.2007.70250
Language英语
Funding ProjectMinistry of Science and Technology, China[5039052006CB] ; National Natural Science Foundation of China[10801131] ; National Natural Science Foundation of China[10631070] ; National Natural Science Foundation of China[60873205] ; JSPS-NSFC
WOS Research AreaBiochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS SubjectBiochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS IDWOS:000271163900005
PublisherIEEE COMPUTER SOC
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/8315
Collection应用数学研究所
Corresponding AuthorWang, Yong
Affiliation1.Chinese Acad Sci, Inst Appl Math, Acad Math & Syst Sci, Beijing 100080, Peoples R China
2.Beijing Foreign Studies Univ, Sch Int Business, Beijing 100081, Peoples R China
3.Osaka Sangyo Univ, Dept Elect Informat & Commun Engn, Osaka 5748530, Japan
Recommended Citation
GB/T 7714
Wang, Yong,Wu, Ling-Yun,Zhang, Ji-Hong,et al. Evaluating Protein Similarity from Coarse Structures[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2009,6(4):583-593.
APA Wang, Yong,Wu, Ling-Yun,Zhang, Ji-Hong,Zhan, Zhong-Wei,Zhang, Xiang-Sun,&Chen, Luonan.(2009).Evaluating Protein Similarity from Coarse Structures.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,6(4),583-593.
MLA Wang, Yong,et al."Evaluating Protein Similarity from Coarse Structures".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 6.4(2009):583-593.
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