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Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites

文献类型：期刊论文

作者Hu, Lun1; Hu, Pengwei2; Luo, Xin3,4; Yuan, Xiaohui1; You, Zhu-Hong5
刊名IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
出版日期2020-11-01
卷号17期号:6页码:2017-2028
关键词HIV-1 protease substrate specificity coevolving information cleavage site prediction
ISSN号1545-5963
DOI10.1109/TCBB.2019.2914208
通讯作者Luo, Xin(luoxin21@cigit.ac.cn) ; You, Zhu-Hong(zhuhongyou@ms.xjb.ac.cn)
英文摘要Human immunodeficiency virus 1 (HIV-1) protease (PR) plays a crucial role in the maturation of the virus. The study of substrate specificity of HIV-1 PR as a new endeavor strives to increase our ability to understand how HIV-1 PR recognizes its various cleavage sites. To predict HIV-1 PR cleavage sites, most of the existing approaches have been developed solely based on the homogeneity of substrate sequence information with supervised classification techniques. Although efficient, these approaches are found to be restricted to the ability of explaining their results and probably provide few insights into the mechanisms by which HIV-1 PR cleaves the substrates in a site-specific manner. In this work, a coevolutionary pattern-based prediction model for HIV-1 PR cleavage sites, namely EvoCleave, is proposed by integrating the coevolving information obtained from substrate sequences with a linear SVM classifier. The experiment results showed that EvoCleave yielded a very promising performance in terms of ROC analysis and f-measure. We also prospectively assessed the biological significance of coevolutionary patterns by applying them to study three fundamental issues of HIV-1 PR cleavage site. The analysis results demonstrated that the coevolutionary patterns offered valuable insights into the understanding of substrate specificity of HIV-1 PR.
资助项目National Natural Science Foundation of China[61602352] ; Chongqing Research Program of Technology Innovation and Application[cstc2017rgzn-zdyfX0020] ; Chongqing Research Program of Technology Innovation and Application[cstc2017zdcy-zdyf0554] ; Chongqing Research Program of Technology Innovation and Application[cstc2017rgzn-zdyf0118] ; Chongqing Cultivation Program of Innovation and Entrepreneurship Demonstration Group[cstc2017kjrccxcytd0149] ; Chongqing Overseas Scholars Innovation Program[cx2017012] ; Chongqing Overseas Scholars Innovation Program[cx2018011] ; Pioneer Hundred Talents Program of Chinese Academy of Sciences ; NSFC Excellent Young Scholars Program[61722212]
WOS研究方向Biochemistry & Molecular Biology ; Computer Science ; Mathematics
语种英语
WOS记录号WOS:000597841800017
出版者IEEE COMPUTER SOC
源URL[http://119.78.100.138/handle/2HOD01W0/12621]  
专题中国科学院重庆绿色智能技术研究院
通讯作者Luo, Xin; You, Zhu-Hong
作者单位1.Wuhan Univ Technol, Sch Comp Sci & Technol, Wuhan 430079, Peoples R China
2.Hong Kong Polytech Univ, Dept Comp, Hong Kong, Peoples R China
3.Chinese Acad Sci, Chongqing Engn Res Ctr Big Data Applicat Smart Ci, Chongqing Inst Green & Intelligent Technol, Chongqing 400714, Peoples R China
4.Chinese Acad Sci, Key Lab Big Data & Intelligent Comp, Chongqing Inst Green & Intelligent Technol, Chongqing 400714, Peoples R China
5.Chinese Acad Sci, Tech Inst Phys & Chem, Urumqi 830001, Peoples R China
推荐引用方式
GB/T 7714		 Hu, Lun,Hu, Pengwei,Luo, Xin,et al. Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2020,17(6):2017-2028.
APA Hu, Lun,Hu, Pengwei,Luo, Xin,Yuan, Xiaohui,&You, Zhu-Hong.(2020).Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,17(6),2017-2028.
MLA Hu, Lun,et al."Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 17.6(2020):2017-2028.

入库方式： OAI收割

来源：重庆绿色智能技术研究院

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