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Updated: Jul 15, 2026
11:34
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
Published on: August 9, 2019
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
Michael Terribilini1, Jeffry D Sander, Jae-Hyung Lee
1Department of Genetics, Development & Cell Biology, Bioinformatics & Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA.
Nucleic Acids Research
|May 8, 2007
Summary
RNABindR is a web tool that identifies protein regions binding to RNA. It analyzes known structures and predicts binding sites in new proteins, aiding biological process research.
Area of Science:
- Structural biology
- Bioinformatics
- Molecular biology
Background:
- Protein-RNA interactions are crucial for biological processes.
- Identifying these interactions is key to understanding molecular mechanisms.
Purpose of the Study:
- To introduce RNABindR, a web server for identifying and predicting RNA-binding residues.
- To provide tools for analyzing known protein-RNA complexes and predicting binding sites in novel proteins.
Main Methods:
- Utilizing a distance cutoff to identify RNA-contacting amino acids in Protein Data Bank (PDB) structures.
- Employing a Naive Bayes classifier trained on PDB data for prediction in unknown protein structures.
- Visualizing RNA-binding residues using Jmol in 3D structural context.
Main Results:
- RNABindR successfully identifies RNA-binding residues in known protein-RNA complexes.
- The server provides predictions with high specificity and sensitivity for proteins with unknown structures.
- A user-friendly web interface with visualization tools is available.
Conclusions:
- RNABindR offers a valuable resource for researchers studying protein-RNA interactions.
- The tool aids in deciphering biological mechanisms involving RNA-binding proteins.
- RNABindR is freely accessible for research purposes.
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