RISP: A web-based server for prediction of RNA-binding sites in proteins

Authors:
Jing Tong;Peng Jiang;Zu-hong Lu
Affiliations:
State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China;State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China;State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
Venue:
Computer Methods and Programs in Biomedicine
Year:
2008

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Abstract

Protein-RNA interactions play significant roles in a number of biological activities, such as protein synthesis, regulation of gene expression. Here we propose a hybrid RISP (RNA-interaction site prediction) method, using support vector machine (SVM) in conjunction with evolutionary information of amino acid sequences in terms of their position-specific scoring matrices (PSSMs) for prediction of RNA-binding sites. The results show that our RISP method has 72.2% net prediction (NP) (61.0% sensitivity and 83.3% specificity). When compared with previous studies, this novel method appears more accurate and better generalization abilities. RISP is freely available at http://grc.seu.edu.cn/RISP. Given a protein sequence, RISP decides whether residue in the protein is RNA-binding or not (optimal prediction), and gives the confidence value, 'high specificity' prediction and 'high sensitivity' prediction.