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Evaluating Protein Similarity from Coarse Structures

文献类型：期刊论文

作者Wang, Yong1; Wu, Ling-Yun1; Zhang, Ji-Hong2; Zhan, Zhong-Wei; Zhang, Xiang-Sun1; Chen, Luonan3
刊名IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
出版日期2009-10-01
卷号6期号:4页码:583-593
关键词Protein structure structure comparison protein surface
ISSN号1545-5963
DOI10.1109/TCBB.2007.70250
英文摘要To 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.
资助项目Ministry 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研究方向Biochemistry & Molecular Biology ; Computer Science ; Mathematics
语种英语
WOS记录号WOS:000271163900005
出版者IEEE COMPUTER SOC
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/8314]  
专题应用数学研究所
通讯作者Wang, Yong
作者单位1.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
推荐引用方式
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.

入库方式： OAI收割

来源：数学与系统科学研究院

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