title: 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.
authors.affiliation: Department of Genetics, Development & Cell Biology, Bioinformatics & Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Terribilini
authors.forename: Jeffry D
authors.initials: JD
authors.lastname: Sander
authors.forename: Jae-Hyung
authors.initials: JH
authors.lastname: Lee
authors.forename: Peter
authors.initials: P
authors.lastname: Zaback
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: Vasant
authors.initials: V
authors.lastname: Honavar
authors.forename: Drena
authors.initials: D
authors.lastname: Dobbs
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D001499:Bayes Theorem; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins; D012313:RNA