Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features

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

	Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features
	Chen, Zhen ; Zhou, Yuan 1; Zhang, Ziding 1; Song, Jiangning 2,3
刊名	BRIEFINGS IN BIOINFORMATICS
	2015-07-01
卷号	16 期号:4 页码:640-657
关键词	protein ubiqutination bioinformatics tool development species-specific ubiquitination sites sequence analysis feature selection
英文摘要	Protein ubiquitination is one of the most important reversible post-translational modifications (PTMs). In many biochemical, pathological and pharmaceutical studies on understanding the function of proteins in biological processes, identification of ubiquitination sites is an important first step. However, experimental approaches for identifying ubiquitination sites are often expensive, labor-intensive and time-consuming, partly due to the dynamics and reversibility of ubiquitination. In silico prediction of ubiquitination sites is potentially a useful strategy for whole proteome annotation. A number of bioinformatics approaches and tools have recently been developed for predicting protein ubiquitination sites. However, these tools have different methodologies, prediction algorithms, functionality and features, which complicate their utility and application. The purpose of this review is to aid users in selecting appropriate tools for specific analyses and circumstances. We first compared five popular webservers and standalone software options, assessing their performance on four up-to-date ubiquitination benchmark datasets from Saccharomyces cerevisiae, Homo sapiens, Mus musculus and Arabidopsis thaliana. We then discussed and summarized these tools to guide users in choosing among the tools efficiently and rapidly. Finally, we assessed the importance of features of existing tools for ubiquitination site prediction, ranking them by performance. We also discussed the features that make noticeable contributions to species-specific ubiquitination site prediction.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biochemical Research Methods ; Mathematical & Computational Biology
研究领域[WOS]	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
关键词[WOS]	AMINO-ACID PAIRS ; POSTTRANSLATIONAL MODIFICATIONS ; PROTEIN UBIQUITINATION ; ROC CURVES ; UBIQUITYLATION ; SEQUENCE ; IDENTIFICATION ; DEGRADATION ; REGIONS
收录类别	SCI
语种	英语
WOS记录号	WOS:000359083200008
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/834782/1510]
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.Monash Univ, Fac Med, Monash Bioinformat Platform, Clayton, Vic 3800, Australia 3.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Beijing 100864, Peoples R China
推荐引用方式 GB/T 7714	Chen, Zhen,Zhou, Yuan,Zhang, Ziding,et al. Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features[J]. BRIEFINGS IN BIOINFORMATICS,2015,16(4):640-657.
APA	Chen, Zhen,Zhou, Yuan,Zhang, Ziding,&Song, Jiangning.(2015).Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features.BRIEFINGS IN BIOINFORMATICS,16(4),640-657.
MLA	Chen, Zhen,et al."Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features".BRIEFINGS IN BIOINFORMATICS 16.4(2015):640-657.