Identification of protein-RNA interaction sites using the information of spatial adjacent residues

Protein-RNA interactions play an important role in numbers of fundamental cellular processes such as RNA splicing, transport and translation, protein synthesis and certain RNA-mediated enzymatic processes. The more knowledge of Protein-RNA recognition can not only help to understand the regulatory mechanism, the site-directed mutagenesis and regulation of RNA-protein complexes in biological systems, but also have a vitally effecting for rational drug design.

Based on the information of spatial adjacent residues, novel feature extraction methods were proposed to predict protein-RNA interaction sites with SVM-KNN classifier. The total accuracies of spatial adjacent residue profile feature and spatial adjacent residues weighted accessibility solvent area feature are 78%, 67.07% respectively in 5-fold cross-validation test, which are 1.4%, 3.79% higher than that of sequence neighbour residue profile feature and sequence neighbour residue accessibility solvent area feature.

The results indicate that the performance of feature extraction method using the spatial adjacent information is superior to the sequence neighbour information approach. The performance of SVM-KNN classifier is little better than that of SVM. The feature extraction method of spatial adjacent information with SVM-KNN is very effective for identifying protein-RNA interaction sites and may at least play a complimentary role to the existing methods.