Rnabindr: a Server for Analyzing and Predicting Rna-binding Sites in Proteins.
From: Department of Genetics, Development & Cell Biology, Bioinformatics & Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA.
Nucleic acids research
- Publish Date: Jul 2007
- ISSN: 1362-4962
- Volume: 35
- Issue: Web Server issue
- Pages: W578-84
- Medium: Internet
- Language: English
- Citation (JAMA): Terribilini Michael, Sander Jeffry D, Lee Jae-Hyung, et al. Rnabindr: a Server for Analyzing and Predicting Rna-binding Sites in Proteins.. Nucleic Acids Res. Jul 2007;35:W578-84
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.
Mesh Headings (Keywords): Amino Acid Motifs, Amino Acid Sequence, Amino Acids, Animals, Bayes Theorem, Binding Sites, Computational Biology, Databases, Protein, Internet, Models, Molecular, Molecular Sequence Data, Protein Conformation, Proteins, RNA, Software
Check for Full Text / PubMed Unique Identifier (PMID): 17483510
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