title: iPTM-mLys: identifying multiple lysine PTM sites and their different types.
abstract: Post-translational modification, abbreviated as PTM, refers to the change of the amino acid side chains of a protein after its biosynthesis. Owing to its significance for in-depth understanding various biological processes and developing effective drugs, prediction of PTM sites in proteins have currently become a hot topic in bioinformatics. Although many computational methods were established to identify various single-label PTM types and their occurrence sites in proteins, no method has ever been developed for multi-label PTM types. As one of the most frequently observed PTMs, the K-PTM, namely, the modification occurring at lysine (K), can be usually accommodated with many different types, such as 'acetylation', 'crotonylation', 'methylation' and 'succinylation'. Now we are facing an interesting challenge: given an uncharacterized protein sequence containing many K residues, which ones can accommodate two or more types of PTM, which ones only one, and which ones none?
  
  
  
  To address this problem, a multi-label predictor called IPTM-MLYS: has been developed. It represents the first multi-label PTM predictor ever established. The novel predictor is featured by incorporating the sequence-coupled effects into the general PseAAC, and by fusing an array of basic random forest classifiers into an ensemble system. Rigorous cross-validations via a set of multi-label metrics indicate that the first multi-label PTM predictor is very promising and encouraging.
  
  
  
  For the convenience of most experimental scientists, a user-friendly web-server for iPTM-mLys has been established at http://www.jci-bioinfo.cn/iPTM-mLys, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
  
  
  
  wqiu@gordonlifescience.org, xxiao@gordonlifescience.org, kcchou@gordonlifescience.orgSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Computer Department, Jingdezhen Ceramic Institute, Jingdezhen 333403, China, Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia MO, USA; Computational Biology, Gordon Life Science Institute, Boston, MA 02478, USA.
authors.forename: Wang-Ren
authors.initials: WR
authors.lastname: Qiu
authors.affiliation: Computer Department, Jingdezhen Ceramic Institute, Jingdezhen 333403, China.
authors.forename: Bi-Qian
authors.initials: BQ
authors.lastname: Sun
authors.affiliation: Computer Department, Jingdezhen Ceramic Institute, Jingdezhen 333403, China, Computational Biology, Gordon Life Science Institute, Boston, MA 02478, USA.
authors.forename: Xuan
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Computer Department, Jingdezhen Ceramic Institute, Jingdezhen 333403, China.
authors.forename: Zhao-Chun
authors.initials: ZC
authors.lastname: Xu
authors.affiliation: Computational Biology, Gordon Life Science Institute, Boston, MA 02478, USA, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D000596:Amino Acids; D000818:Animals; D006801:Humans; D008239:Lysine; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000378:metabolism
chemical_list: D000596:Amino Acids; D011506:Proteins; D008239:Lysine