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

Background: 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.results: 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.conclusions: 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. © 2011 chen et al; licensee biomed central ltd.