RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein–RNA complexes and predicts RNA-binding residues in proteins of unknown structure. RNABindR uses a distance cutoff to identify which amino acids contact RNA in solved complex structures (from the Protein Data Bank) and provides a labeled amino acid sequence and a Jmol graphical viewer in which RNA-binding residues are displayed in the context of the three-dimensional structure. Alternatively, RNABindR can use a Naive Bayes classifier trained on a non-redundant set of protein–RNA complexes from the PDB to predict which amino acids in a protein sequence of unknown structure are most likely to bind RNA. RNABindR automatically displays ‘high specificity’ and ‘high sensitivity’ predictions of RNA-binding residues. RNABindR is freely available at http://bindr.gdcb.iastate.edu/RNABindR.