title: Prediction of flavin mono-nucleotide binding sites using modified PSSM profile and ensemble support vector machine.
abstract: Flavin mono-nucleotide (FMN) closely evolves in many biological processes. In this study, a computational method was proposed to identify FMN binding sites based on amino acid sequences of proteins only. A modified Position Specific Score Matrix was used to characterize the local environmental sequence information, and a visible improvement of performance was obtained. Also, the ensemble SVM was applied to solve the imbalanced data problem. Additionally, an independent dataset was built to evaluate the practical performance of the method, and a satisfactory accuracy of 87.87% was achieved. It demonstrates that the method is effective in predicting FMN-binding sites.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, PR China.
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.forename: Gang
authors.initials: G
authors.lastname: Mi
authors.forename: Cuicui
authors.initials: C
authors.lastname: Wang
authors.forename: Yongqing
authors.initials: Y
authors.lastname: Zhang
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.forename: Yanzhi
authors.initials: Y
authors.lastname: Guo
authors.forename: Xuemei
authors.initials: X
authors.lastname: Pu
authors.forename: Menglong
authors.initials: M
authors.lastname: Li
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D016208:Databases, Factual; D005486:Flavin Mononucleotide / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D056510:Position-Specific Scoring Matrices; D012372:ROC Curve; D015203:Reproducibility of Results; D013223:Statistics as Topic; D060388:Support Vector Machine
chemical_list: D005486:Flavin Mononucleotide