pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach

Journal of Theoretical Biology
Jianhua JiaKuo-Chen Chou

Abstract

Being one type of post-translational modifications (PTMs), protein lysine succinylation is important in regulating varieties of biological processes. It is also involved with some diseases, however. Consequently, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence having many Lys residues therein, which ones can be succinylated, and which ones cannot? To address this problem, we have developed a predictor called pSuc-Lys through (1) incorporating the sequence-coupled information into the general pseudo amino acid composition, (2) balancing out skewed training dataset by random sampling, and (3) constructing an ensemble predictor by fusing a series of individual random forest classifiers. Rigorous cross-validations indicated that it remarkably outperformed the existing methods. A user-friendly web-server for pSuc-Lys has been established at http://www.jci-bioinfo.cn/pSuc-Lys, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can also be used to analyze many other problems in computat...Continue Reading

References

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Jul 22, 2010·Journal of Biomolecular Structure & Dynamics·Hong-Bin Shen, Kuo-Chen Chou
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Jan 11, 2013·Nucleic Acids Research·Wei ChenKuo-Chen Chou

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Citations

Apr 27, 2016·Meta Gene·Selvaraman NagamaniKarthikeyan Muthusamy
May 29, 2016·Journal of Theoretical Biology·Z GhanbariM Izadyar
Jun 14, 2016·Journal of Theoretical Biology·Cheng-Hong YangLi-Yeh Chuang
Jun 21, 2016·Journal of Theoretical Biology·Mohammad H OlyaeeMahdi Yaghoobi
Jun 24, 2016·Bioinformatics·Wang-Ren QiuKuo-Chen Chou
Aug 25, 2016·Journal of Theoretical Biology·Lei YangYingli Lv
Sep 26, 2016·Computational Biology and Chemistry·Shu-Bo Zhang, Qiang-Rong Tang
Oct 30, 2016·International Journal of Molecular Sciences·Tzu-Hao Kuo, Kuo-Bin Li
Feb 18, 2017·International Journal of Molecular Sciences·Chengchao WuXuehai Hu
Jun 26, 2017·Journal of Theoretical Biology·Ehsan Saghapour, Mohammadreza Sehhati
Mar 20, 2018·Bioinformatics·Matteo Lo MonteAndrea Rosario Beccari
Mar 30, 2018·Molecular Genetics and Genomics : MGG·Shanxin ZhangZhenghong Xu
Nov 28, 2017·Scientific Reports·Thales Francisco Mota CarvalhoFabio Ribeiro Cerqueira
Sep 30, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Wenzheng BaoDe-Shuang Huang
Sep 22, 2017·PloS One·Ehsan SaghapourMohammadreza Sehhati
Dec 24, 2018·Briefings in Functional Genomics·Wenying HeQuan Zou
Feb 16, 2019·Journal of Computational Chemistry·Sandra Romero-MolinaElsa Sanchez-Garcia
Nov 6, 2018·Current Drug Targets·Surovi SaikiaRajeev Sarmah
Apr 27, 2019·Molecular Omics·Hussam J Al-BarakatiDukka B Kc

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