ArticleNucleic acids research2009
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- RNApedia: a database of structural protein-RNA interactions.Frontiers in bioinformatics · 2026Article
- Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- RNA-protein interaction prediction without high-throughput data: An overview and benchmark ofComputational and structural biotechnology journal · 2024Article
- BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic acids research · 2024Article
- ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation.Nucleic acids research · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- RNAInter in 2020: RNA interactome repository with increased coverage and annotation.Nucleic acids research · 2020Article
- Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS.Molecules (Basel, Switzerland) · 2019Article
- Alternative splicing and the evolution of phenotypic novelty.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- A Brief Review of RNA-Protein Interaction Database Resources.Non-coding RNA · 2017Review
- RAID v2.0: an updated resource of RNA-associated interactions across organisms.Nucleic acids research · 2017Article
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Structure based approach for understanding organism specific recognition of protein-RNA complexes.Biology direct · 2015Article
- RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction.RNA (New York, N.Y.) · 2014Article
- Prediction of RNA binding proteins comes of age from low resolution to high resolution.Molecular bioSystems · 2013Review
- BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.Nucleic acids research · 2013Article
- PRince: a web server for structural and physicochemical analysis of protein-RNA interface.Nucleic acids research · 2012Article
- Virtual interactomics of proteins from biochemical standpoint.Molecular biology international · 2012Article
- PRIDB: a Protein-RNA interface database.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
We present a new database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases. The database consists of a classification of binding sites derived from protein-RNA complexes. Each binding site is assigned to a cluster of similar binding sites in other protein-RNA complexes. Cluster members share similar spatial arrangements of physico-chemical properties, thus can reveal novel similarity between proteins and RNAs with different sequences and folds. The clusters provide 3D consensus binding patterns important for protein-nucleotide recognition. The database search engine allows two types of useful queries: first, given a PDB code of a protein-RNA complex, RsiteDB can detail and classify the properties of the protein binding pockets accommodating extruded RNA nucleotides not involved in local RNA base pairing. Second, given an unbound protein structure, RsiteDB can perform an on-line structural search against the constructed database of 3D consensus binding patterns. Regions similar to known patterns are predicted to serve as binding sites. Alignment of the query to these patterns with their corresponding RNA nucleotides allows making unique predictions of the protein-RNA interactions at the atomic level of detail. This database is accessible at http://bioinfo3d.cs.tau.ac.il/RsiteDB.
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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.