Discrimination of outer membrane proteins by a new measure of information discrepancy

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	Discrimination of outer membrane proteins by a new measure of information discrepancy
	Wu, Zikai ; Feng, Enmin ; Wang, Yong; Chen, Luonan
	2007
发表期刊	PROTEIN AND PEPTIDE LETTERS
ISSN	0929-8665
卷号	14 期号:1 页码:37-44
摘要	Discriminating outer membrane proteins for globular proteins (GPs) and other types of membrane proteins from genomic sequences is an important and hot topic. In this paper, a measure based on information discrepancy is proposed and applied to the discrimination of outer membrane proteins. It differs from previous methods which are based on amino acid composition. Our approach focuses on the comparison of subsequence distributions and takes into account the effect of residue order in protein primary structures. As a result, the new approach outperforms all previous methods on the same benchmark datasets. In particular, we show that the proposed approach has correctly identified the outer membrane proteins at an accuracy of 99% for the training set of 337 proteins and has correctly excluded the GPs at an accuracy of 86% in a non-redundant dataset of 668 proteins. Furthermore, this method is able to correctly exclude alpha-helical membrane proteins at an accuracy of 100%.
关键词	outer membrane protein subsequence distribution FDOD measure
语种	英语
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000245376700007
出版者	BENTHAM SCIENCE PUBL LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/4101
专题	应用数学研究所
通讯作者	Wu, Zikai
作者单位	1.Dalian Univ Technol, Dept Appl Math, Dalian 116024, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing 100080, Peoples R China 3.Osaka Sangyo Univ, Dept Elect Informat & Commun, Osaka 5748530, Japan 4.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
推荐引用方式 GB/T 7714	Wu, Zikai,Feng, Enmin,Wang, Yong,et al. Discrimination of outer membrane proteins by a new measure of information discrepancy[J]. PROTEIN AND PEPTIDE LETTERS,2007,14(1):37-44.
APA	Wu, Zikai,Feng, Enmin,Wang, Yong,&Chen, Luonan.(2007).Discrimination of outer membrane proteins by a new measure of information discrepancy.PROTEIN AND PEPTIDE LETTERS,14(1),37-44.
MLA	Wu, Zikai,et al."Discrimination of outer membrane proteins by a new measure of information discrepancy".PROTEIN AND PEPTIDE LETTERS 14.1(2007):37-44.