title: Homology-free prediction of functional class of proteins and peptides by support vector machines.
abstract: Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy and Center for Computational Science and Engineering, National University of Singapore, Blk S16, Level 8, 3 Science Drive 2, Singapore.
authors.forename: F
authors.initials: F
authors.lastname: Zhu
authors.forename: L Y
authors.initials: LY
authors.lastname: Han
authors.forename: X
authors.initials: X
authors.lastname: Chen
authors.forename: H H
authors.initials: HH
authors.lastname: Lin
authors.forename: S
authors.initials: S
authors.lastname: Ong
authors.forename: B
authors.initials: B
authors.lastname: Xie
authors.forename: H L
authors.initials: HL
authors.lastname: Zhang
authors.forename: Y Z
authors.initials: YZ
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D010455:Peptides / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins