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

Michael Terribilini, Jeffry D. Sander, Jae Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, Drena Dobbs

Research output: Contribution to journalArticle

142 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)W578-W584
JournalNucleic acids research
Volume35
Issue numberSUPPL.2
DOIs
StatePublished - Jul 1 2007

    Fingerprint

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Terribilini, M., Sander, J. D., Lee, J. H., Zaback, P., Jernigan, R. L., Honavar, V., & Dobbs, D. (2007). RNABindR: A server for analyzing and predicting RNA-binding sites in proteins. Nucleic acids research, 35(SUPPL.2), W578-W584. https://doi.org/10.1093/nar/gkm294