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  4. 期刊论文
ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences

文献类型：期刊论文

作者Chen, Zhen1; Wang, Yanying1; Zhai, Ya-Feng1; Song, Jiangning2,3,4; Zhang, Ziding1
刊名MOLECULAR BIOSYSTEMS
出版日期2013
卷号9期号:9页码:2213-2222
英文摘要As one of the most important trace elements within an organism, zinc has been shown to be involved in numerous biological processes and closely implicated in various diseases. The zinc ion is important for proteins to perform their functional roles. To provide in-depth functional annotation of zinc-binding proteins, an initial but crucial step is the accurate recognition of zinc-binding sites. Motivated by the biological importance of zinc, we propose a new method called ZincExplorer to predict zinc-binding sites from protein sequences. ZincExplorer is a hybrid method that can accurately predict zinc-binding sites from protein sequences. It integrates the outputs of three different types of predictors, namely, SVM-, cluster-and template-based predictors. Four types of zinc-binding amino acids CHEDs (i.e. CYS, HIS, ASP and GLU) could be predicted using ZincExplorer. It achieved a high AURPC (Area Under Recall-Precision Curve) of 0.851, and a precision of 85.6% (specificity = 98.4%, MCC = 0.747) at the 70.0% recall for the CHEDs on the 5-fold cross-validation test. When tested on an independent dataset containing 2023 zinc-binding CHEDs and 14 493 non-zinc-binding CHEDs, it achieved about 3-8% higher AURPC in comparison to two other sequence-based predictors. Moreover, ZincExplorer could also identify the interdependent relationships (IRs) of the predicted zinc-binding sites bound to the same zinc ion, which makes it a useful tool for providing in-depth zinc-binding site annotation.
WOS标题词Science & Technology ; Life Sciences & Biomedicine
类目[WOS]Biochemistry & Molecular Biology
研究领域[WOS]Biochemistry & Molecular Biology
关键词[WOS]AMINO-ACID PAIRS ; CATALYTIC RESIDUES ; ALIGNMENTS ; GPS
收录类别SCI
语种英语
WOS记录号WOS:000322447600004
公开日期2014-11-23
源URL[http://124.16.173.210/handle/311007/429]  
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, 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,Wang, Yanying,Zhai, Ya-Feng,et al. ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences[J]. MOLECULAR BIOSYSTEMS,2013,9(9):2213-2222.
APA Chen, Zhen,Wang, Yanying,Zhai, Ya-Feng,Song, Jiangning,&Zhang, Ziding.(2013).ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.MOLECULAR BIOSYSTEMS,9(9),2213-2222.
MLA Chen, Zhen,et al."ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences".MOLECULAR BIOSYSTEMS 9.9(2013):2213-2222.

入库方式： OAI收割

来源：天津工业生物技术研究所

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