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

143 Citations (Scopus)

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

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Binding Sites
RNA
Proteins
Biological Phenomena
Amino Acids
Amino Acid Sequence
Databases
Sensitivity and Specificity

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
Terribilini, Michael ; Sander, Jeffry D. ; Lee, Jae Hyung ; Zaback, Peter ; Jernigan, Robert L. ; Honavar, Vasant ; Dobbs, Drena. / RNABindR : A server for analyzing and predicting RNA-binding sites in proteins. In: Nucleic acids research. 2007 ; Vol. 35, No. SUPPL.2. pp. W578-W584.
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Terribilini, M, Sander, JD, Lee, JH, Zaback, P, Jernigan, RL, Honavar, V & Dobbs, D 2007, 'RNABindR: A server for analyzing and predicting RNA-binding sites in proteins', Nucleic acids research, vol. 35, no. SUPPL.2, pp. W578-W584. https://doi.org/10.1093/nar/gkm294

RNABindR : A server for analyzing and predicting RNA-binding sites in proteins. / Terribilini, Michael; Sander, Jeffry D.; Lee, Jae Hyung; Zaback, Peter; Jernigan, Robert L.; Honavar, Vasant; Dobbs, Drena.

In: Nucleic acids research, Vol. 35, No. SUPPL.2, 01.07.2007, p. W578-W584.

Research output: Contribution to journalArticle

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Terribilini M, Sander JD, Lee JH, Zaback P, Jernigan RL, Honavar V et al. RNABindR: A server for analyzing and predicting RNA-binding sites in proteins. Nucleic acids research. 2007 Jul 1;35(SUPPL.2):W578-W584. https://doi.org/10.1093/nar/gkm294