ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition

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	ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition
	Wang, JY(王靖琰) ; Li, YP(李勇平) ; Wang, QQ ; You, XG ; Man, JJ ; Wang, C ; Gao, X
刊名	COMPUTERS IN BIOLOGY AND MEDICINE
	2012
卷号	42 期号:5
ISSN号	0010-4825
英文摘要	Knowing the type of an uncharacterized membrane protein often provides a useful clue in both basic research and drug discovery. With the explosion of protein sequences generated in the post genomic era, determination of membrane protein types by experimental methods is expensive and time consuming. It therefore becomes important to develop an automated method to find the possible types of membrane proteins. In view of this, various computational membrane protein prediction methods have been proposed. They extract protein feature vectors, such as PseAAC (pseudo amino acid composition) and PsePSSM (pseudo position-specific scoring matrix) for representation of protein sequence, and then learn a distance metric for the KNN (K nearest neighbor) or NN (nearest neighbor) classifier to predicate the final type. Most of the metrics are learned using linear dimensionality reduction algorithms like Principle Components Analysis (PCA) and Linear Discriminant Analysis (LDA). Such metrics are common to all the proteins in the dataset. In fact, they assume that the proteins lie on a uniform distribution, which can be captured by the linear dimensionality reduction algorithm. We doubt this assumption, and learn local metrics which are optimized for local subset of the whole proteins. The learning procedure is iterated with the protein clustering. Then a novel ensemble distance metric is given by combining the local metrics through Tikhonov regularization. The experimental results on a benchmark dataset demonstrate the feasibility and effectiveness of the proposed algorithm named ProClusEnsem. (C) 2012 Elsevier Ltd. All rights reserved.
语种	英语
WOS记录号	WOS:000303290500007
公开日期	2013-12-05
内容类型	期刊论文
源URL	[http://ir.sinap.ac.cn/handle/331007/13258]
专题	上海应用物理研究所_中科院上海应用物理研究所2011-2017年
推荐引用方式 GB/T 7714	Wang, JY,Li, YP,Wang, QQ,et al. ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition[J]. COMPUTERS IN BIOLOGY AND MEDICINE,2012,42(5).
APA	Wang, JY.,Li, YP.,Wang, QQ.,You, XG.,Man, JJ.,...&Gao, X.(2012).ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition.COMPUTERS IN BIOLOGY AND MEDICINE,42(5).
MLA	Wang, JY,et al."ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition".COMPUTERS IN BIOLOGY AND MEDICINE 42.5(2012).