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	Classification of protein quaternary structure by functional domain composition
	Yu, XJ; Wang, C; Li, YX
刊名	Bmc bioinformatics
	2006-04-04
卷号	7页码:6
ISSN号	1471-2105
DOI	10.1186/1471-2105-7-187
通讯作者	Li, yx(yxli@sibs.ac.cn)
英文摘要	Background: the number and the arrangement of subunits that form a protein are referred to as quaternary structure. quaternary structure is an important protein attribute that is closely related to its function. proteins with quaternary structure are called oligomeric proteins. oligomeric proteins are involved in various biological processes, such as metabolism, signal transduction, and chromosome replication. thus, it is highly desirable to develop some computational methods to automatically classify the quaternary structure of proteins from their sequences. results: to explore this problem, we adopted an approach based on the functional domain composition of proteins. every protein was represented by a vector calculated from the domains in the pfam database. the nearest neighbor algorithm ( nna) was used for classifying the quaternary structure of proteins from this information. the jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. the overall success rate obtained is 75.17%. additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11% conclusion: compared with the amino acid composition method and blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics.
WOS关键词	AMINO-ACID-COMPOSITION ; SUPPORT VECTOR MACHINE ; SUBCELLULAR-LOCALIZATION ; SWISS-PROT ; PREDICTION ; DATABASE ; PFAM ; ALIGNMENTS ; ALGORITHM ; LOCATION
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000237201700001
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2378659
专题	中国科学院大学
通讯作者	Li, YX
作者单位	1.Chinese Acad Sci, Shanghai Inst Biol Sci, Bioinformat Ctr, Shanghai 200031, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 3.Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China
推荐引用方式 GB/T 7714	Yu, XJ,Wang, C,Li, YX. Classification of protein quaternary structure by functional domain composition[J]. Bmc bioinformatics,2006,7:6.
APA	Yu, XJ,Wang, C,&Li, YX.(2006).Classification of protein quaternary structure by functional domain composition.Bmc bioinformatics,7,6.
MLA	Yu, XJ,et al."Classification of protein quaternary structure by functional domain composition".Bmc bioinformatics 7(2006):6.

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