ArticleNucleic acids research2007
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 183 citations in OpenAlex.
- DyProL: Dynamic Ensemble Representation Learning for Protein-Nucleic Acid Binding Site Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A novel RNA-binding activity of ECD contributes to U5 snRNP stability and pre-mRNA splicing.Nucleic acids research · 2026Article
- TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.Communications biology · 2025Article
- Synchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates.Protein science : a publication of the Protein Society · 2024Article
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- EPDRNA: A Model for Identifying DNA-RNA Binding Sites in Disease-Related Proteins.The protein journal · 2024Article
- A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond.Briefings in bioinformatics · 2024Review
- Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches.PLoS computational biology · 2023Article
- GeoBind: segmentation of nucleic acid binding interface on protein surface with geometric deep learning.Nucleic acids research · 2023Article
- HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins.Nucleic acids research · 2023Article
- Artificial intelligence methods enhance the discovery of RNA interactions.Frontiers in molecular biosciences · 2022Review
- Evolution of a Cytoplasmic Determinant: Evidence for the Biochemical Basis of Functional Evolution of the Novel Germ Line Regulator Oskar.Molecular biology and evolution · 2021Article
- Article
- Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type.International journal of molecular sciences · 2020Review
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
- How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.Molecular cell · 2020Review
- Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Partner-specific prediction of RNA-binding residues in proteins: A critical assessment.Proteins · 2019Article
- Evolutionary Trends in RNA Base Selectivity Within the RNase A Superfamily.Frontiers in pharmacology · 2019Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 1 institution in 1 country.
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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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.