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

Date
2007-01-01
Authors
Terribilini, Michael
Sander, Jeffry
Lee, Jae-Hyung
Zaback, Peter
Jernigan, Robert
Honavar, Vasant
Dobbs, Drena
Journal Title
Journal ISSN
Volume Title
Publisher
Altmetrics
Authors
Research Projects
Organizational Units
Journal Issue
Series
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.

Description

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

Keywords
Citation
DOI
Collections