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SVM based prediction of RNA-binding proteins using binding residues and evolutionary information

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title SVM based prediction of RNA-binding proteins using binding residues and evolutionary information
 
Creator Kumar, Manish
Gromiha, M Michael
Raghava, G.P.S.
 
Subject QR Microbiology
 
Description RNA-binding proteins (RBPs) play crucial role in transcription and gene-regulation. This paper describes a support vector machine (SVM) based method for discriminating and classifying RNA-binding and non-binding proteins using sequence features. With the threshold of 30% interacting residues, RNA-binding amino acid prediction method PPRINT achieved the Matthews correlation coefficient (MCC) of 0.32. BLAST and PSI-BLAST identified RBPs with the coverage of 32.63 and 33.16%, respectively, at the e-value of 1e-4. The SVM models developed with amino acid, dipeptide and four-part amino acid compositions showed the MCC of 0.60, 0.46, and 0.53, respectively. This is the first study in which evolutionary information in form of position specific scoring matrix (PSSM) profile has been successfully used for predicting RBPs. We achieved the maximum MCC of 0.62 using SVM model based on PSSM called PSSM-400. Finally, we developed different hybrid approaches and achieved maximum MCC of 0.66. We also developed a method for predicting three subclasses of RNA binding proteins (e.g., rRNA, tRNA, mRNA binding proteins). The performance of the method was also evaluated on an independent dataset of 69 RBPs and 100 non-RBPs (NBPs). An additional benchmarking was also performed using gene ontology (GO) based annotation. Based on the hybrid approach a web-server RNApred has been developed for predicting RNA binding proteins from amino acid sequences (http://www.imtech.res.in/raghava/rnapred/).
 
Publisher Wiley
 
Date 2011
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/7/1/raghava2011.5.pdf
Kumar, Manish and Gromiha, M Michael and Raghava, G.P.S. (2011) SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. Journal of molecular recognition : JMR, 24 (2). pp. 303-13. ISSN 1099-1352
 
Relation http://onlinelibrary.wiley.com/doi/10.1002/jmr.1061/pdf
http://crdd.osdd.net/open/7/