Prediction of Protein-RNA interaction site using SVM-KNN algorithm with spatial information

Abstract

Protein-RNA interactions are vitally important to a number of fundamental cellular processes, including regulation of gene expression such as RNA splicing, transport and translation, protein synthesis and assembly of ribosome. More detailed information on the Protein-RNA interaction is helpful for comprehending the function notation and molecular regulatory mechanism, meanwhile, knowing the knowledge of Protein-RNA recognition can also help the biological scientist and researcher understand the site-directed mutagenesis and drug design. In the present work, we proposed a computational approach, based on SVM-KNN algorithm, with evolutionary information of spatial neighbour residues for prediction of protein-RNA interaction sites. The overall success rate obtained by 5-fold cross-validation is 78.00%, which is comparable or better than other existing methods, indicating our method is very promising for identifying and predicting protein-RNA interaction sites.