Evaluating Protein Similarity from Coarse Structures

doi:10.1109/TCBB.2007.70250

CSpace > 应用数学研究所

	Evaluating Protein Similarity from Coarse Structures
	Wang, Yong1 ; Wu, Ling-Yun1 ; Zhang, Ji-Hong 2; Zhan, Zhong-Wei ; Zhang, Xiang-Sun1 ; Chen, Luonan 3
	2009-10-01
发表期刊	IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN	1545-5963
卷号	6 期号:4 页码:583-593
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.
关键词	Protein structure structure comparison protein surface
DOI	10.1109/TCBB.2007.70250
语种	英语
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
WOS类目	Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS记录号	WOS:000271163900005
出版者	IEEE COMPUTER SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/8315
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.