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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