title: Prediction of protein cleavage site with feature selection by random forest.
abstract: Proteinases play critical roles in both intra and extracellular processes by binding and cleaving their protein substrates. The cleavage can either be non-specific as part of degradation during protein catabolism or highly specific as part of proteolytic cascades and signal transduction events. Identification of these targets is extremely challenging. Current computational approaches for predicting cleavage sites are very limited since they mainly represent the amino acid sequences as patterns or frequency matrices. In this work, we developed a novel predictor based on Random Forest algorithm (RF) using maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). The features of physicochemical/biochemical properties, sequence conservation, residual disorder, amino acid occurrence frequency, secondary structure and solvent accessibility were utilized to represent the peptides concerned. Here, we compared existing prediction tools which are available for predicting possible cleavage sites in candidate substrates with ours. It is shown that our method makes much more reliable predictions in terms of the overall prediction accuracy. In addition, this predictor allows the use of a wide range of proteinases.
authors.affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, PR China.
authors.forename: Bi-Qing
authors.initials: BQ
authors.lastname: Li
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
authors.forename: Kai-Yan
authors.initials: KY
authors.lastname: Feng
authors.forename: Gui-Jun
authors.initials: GJ
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D003663:Decision Trees; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010447:Peptide Hydrolases / Q000737:chemistry; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry; D059748:Proteolysis; D020539:Sequence Analysis, Protein
chemical_list: D010447:Peptide Hydrolases; D046988:Proteasome Endopeptidase Complex