title: ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives.
abstract: Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. Existing prediction methods use randomly selected non-validated sites as non-ubiquitination sites to train ubiquitination site prediction models.
  
  
  
  We propose an evolutionary screening algorithm (ESA) to select effective negatives among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. The ESA selects non-validated sites least likely to be ubiquitination sites as training negatives. Moreover, the ESA and ESA-UbiSite use a set of well-selected physicochemical properties together with a support vector machine for accurate prediction. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy and a Matthews's correlation coefficient of 0.48, better than existing prediction methods. The ESA increased ESA-UbiSite's test accuracy from 0.75 to 0.92 and can improve other post-translational modification site prediction methods.
  
  
  
  An ESA-UbiSite-based web server has been established at http://iclab.life.nctu.edu.tw/iclab_webtools/ESAUbiSite/ .
  
  
  
  syho@mail.nctu.edu.tw.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Jyun-Rong
authors.initials: JR
authors.lastname: Wang
authors.affiliation: Department and Institute of Industrial Engineering and Management, Minghsin University of Science and Technology, Hsinchu 300, Taiwan.
authors.forename: Wen-Lin
authors.initials: WL
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Ming-Ju
authors.initials: MJ
authors.lastname: Tsai
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Kai-Ti
authors.initials: KT
authors.lastname: Hsu
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.|Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Hui-Ling
authors.initials: HL
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.|Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Shinn-Ying
authors.initials: SY
authors.lastname: Ho
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D012984:Software; D060388:Support Vector Machine; D054875:Ubiquitination