Prediction of flavin mono-nucleotide binding sites using modified PSSM profile and ensemble support vector machine

Authors:
Xia Wang;Gang Mi;Cuicui Wang;Yongqing Zhang;Juan Li;Yanzhi Guo;Xuemei Pu;Menglong Li
Affiliations:
College of Chemistry, Sichuan University, Chengdu 610064, PR China;College of Life Science, Sichuan University, Chengdu 610064, PR China;College of Chemistry, Sichuan University, Chengdu 610064, PR China;College of Computer Science, Sichuan University, Chengdu 610064, PR China;College of Chemistry, Sichuan University, Chengdu 610064, PR China;College of Chemistry, Sichuan University, Chengdu 610064, PR China;College of Chemistry, Sichuan University, Chengdu 610064, PR China;College of Chemistry, Sichuan University, Chengdu 610064, PR China
Venue:
Computers in Biology and Medicine
Year:
2012

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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.