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

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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Terribilini M,Sander JD,Lee JH,Zaback P,Jernigan RL,Honavar V,Dobbs D

doi

10.1093/nar/gkm294

subject

Has Abstract

pub_date

2007-07-01 00:00:00

pages

W578-84

issue

Web Server issue

eissn

0305-1048

issn

1362-4962

pii

gkm294

journal_volume

35

pub_type

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