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RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
Nucleic Acids Research
  • Michael Terribilini, Iowa State University
  • Jeffry D. Sander, Iowa State University
  • Jae-Hyung Lee, Iowa State University
  • Peter Zaback, Iowa State University
  • Robert L. Jernigan, Iowa State University
  • Vasant Honavar, Iowa State University
  • Drena Dobbs, Iowa State University
Document Type
Article
Publication Version
Published Version
Publication Date
1-1-2007
DOI
10.1093/nar/gkm294
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.

Comments

This article is from Nucleic Acids Research 35 (2007): W578, doi: 10.1093/nar/gkm294. Posted with permission.

Rights
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
The Authors
Language
en
File Format
application/pdf
Citation Information
Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, et al.. "RNABindR: a server for analyzing and predicting RNA-binding sites in proteins" Nucleic Acids Research Vol. 35 (2007) p. W578 - W584
Available at: http://works.bepress.com/drena-dobbs/33/