hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

CORC > 天津工业生物技术研究所 > 结构生物信息学和整合系统生物学实验室宋江宁 > 期刊论文

	hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties
	Chen, Zhen 1; Zhou, Yuan 1; Song, Jiangning 2,3,4; Zhang, Ziding 1
刊名	BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
	2013-08-01
卷号	1834 期号:8 页码:1461-1467
关键词	Ubiquitination site Post-translational modification Composition of k-spaced amino acid pairs Amino acid physicochemical properties
英文摘要	As one of the most common post-translational modifications, ubiquitination regulates the quantity and function of a variety of proteins. Experimental and clinical investigations have also suggested the crucial roles of ubiquitination in several human diseases. The complicated sequence context of human ubiquitination sites revealed by proteomic studies highlights the need of developing effective computational strategies to predict human ubiquitination sites. Here we report the establishment of a novel human-specific ubiquitination site predictor through the integration of multiple complementary classifiers. Firstly, a Support Vector Machine (SVM) classier was constructed based on the composition of k-spaced amino acid pairs (CKSAAP) encoding, which has been utilized in our previous yeast ubiquitination site predictor. To further exploit the pattern and properties of the ubiquitination sites and their flanking residues, three additional SVM classifiers were constructed using the binary amino acid encoding, the AAindex physicochemical property encoding and the protein aggregation propensity encoding, respectively. Through an integration that relied on logistic regression, the resulting predictor termed hCKSAAP_UbSite achieved an area under ROC curve (AUC) of 0.770 in 5-fold cross-validation test on a class-balanced training dataset. When tested on a class-balanced independent testing dataset that contains 3419 ubiquitination sites, hCKSAAP_UbSite has also achieved a robust performance with an AUC of 0.757. Specifically, it has consistently performed better than the predictor using the CKSAAP encoding alone and two other publicly available predictors which are not human-specific. Given its promising performance in our large-scale datasets, hCKSAAP_UbSite has been made publicly available at our server (http://protein.cau.edu.cnicksaap_ubsite/). (C) 2013 Elsevier B.V. All rights reserved.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biochemistry & Molecular Biology ; Biophysics
研究领域[WOS]	Biochemistry & Molecular Biology ; Biophysics
关键词[WOS]	PROTEIN SEQUENCES ; PAIRS ; IDENTIFICATION ; REPRESENTATION ; UBIQUITYLATION ; DEGRADATION ; SPECIFICITY ; COLLOCATION ; PROTEASOME ; DATABASE
收录类别	SCI
语种	英语
WOS记录号	WOS:000321802200001
公开日期	2014-11-23
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/311007/427]
专题	天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室宋江宁_期刊论文
作者单位	1.China Agr Univ, Coll Biol Sci, State Key Lab Agrobiotechnol, Beijing 100193, Peoples R China 2.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Natl Engn Lab Ind Enzymes, Tianjin 300308, Peoples R China 3.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China 4.Monash Univ, Fac Med, Dept Biochem & Mol Biol, Melbourne, Vic 3800, Australia
推荐引用方式 GB/T 7714	Chen, Zhen,Zhou, Yuan,Song, Jiangning,et al. hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties[J]. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS,2013,1834(8):1461-1467.
APA	Chen, Zhen,Zhou, Yuan,Song, Jiangning,&Zhang, Ziding.(2013).hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS,1834(8),1461-1467.
MLA	Chen, Zhen,et al."hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties".BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 1834.8(2013):1461-1467.