title: Computational prediction of species-specific malonylation sites via enhanced characteristic strategy.
abstract: BACKGROUND
  Protein malonylation is a novel post-translational modification (PTM) which orchestrates a variety of biological processes. Annotation of malonylation in proteomics is the first-crucial step to decipher its physiological roles which are implicated in the pathological processes. Comparing with the expensive and laborious experimental research, computational prediction can provide an accurate and effective approach to the identification of many types of PTMs sites. However, there is still no online predictor for lysine malonylation.
  
  
  RESULTS
  By searching from literature and database, a well-prepared up-to-data benchmark datasets were collected in multiple organisms. Data analyses demonstrated that different organisms were preferentially involved in different biological processes and pathways. Meanwhile, unique sequence preferences were observed for each organism. Thus, a novel malonylation site online prediction tool, called MaloPred, which can predict malonylation for three species, was developed by integrating various informative features and via an enhanced feature strategy. On the independent test datasets, AUC (area under the receiver operating characteristic curves) scores are obtained as 0.755, 0.827 and 0.871 for Escherichia coli ( E.coli ), Mus musculus ( M.musculus ) and Homo sapiens ( H.sapiens ), respectively. The satisfying results suggest that MaloPred can provide more instructive guidance for further experimental investigation of protein malonylation.
  
  
  METHODS
  http://bioinfo.ncu.edu.cn/MaloPred.aspx .
  
  
  BACKGROUND
  jdqiu@ncu.edu.cn.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang, China.|Department of sciences, Nanchang Institute of Technology, Nanchang, China.
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Wang
authors.affiliation: Department of Mathematics, Nanchang University, Nanchang, China.
authors.forename: Shao-Ping
authors.initials: SP
authors.lastname: Shi
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang, China.
authors.forename: Hao-Dong
authors.initials: HD
authors.lastname: Xu
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang, China.
authors.forename: Ping-Ping
authors.initials: PP
authors.lastname: Wen
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang, China.
authors.forename: Jian-Ding
authors.initials: JD
authors.lastname: Qiu
mesh_terms: D000818:Animals; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D008239:Lysine / Q000378:metabolism*; D008314:Malonates / Q000378:metabolism*; D051379:Mice; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D012372:ROC Curve; D012984:Software
chemical_list: D008314:Malonates; C030290:malonic acid; D008239:Lysine