ArticleRNA (New York, N.Y.)2019
A structure-based model for the prediction of protein-RNA binding affinity.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition.Current research in structural biology · 2026Article
- PANTHER Score: Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression.RNA (New York, N.Y.) · 2026Article
- RNApedia: a database of structural protein-RNA interactions.Frontiers in bioinformatics · 2026Article
- CAP: Commutative algebra prediction of protein-nucleic acid binding affinities.Machine learning: science and technology · 2025Article
- Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants.Nucleic acids research · 2022Article
- A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism inJournal of bacteriology · 2021Article
- The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.Frontiers in molecular biosciences · 2021Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-RNA recognition is highly affinity-driven and regulates a wide array of cellular functions. In this study, we have curated a binding affinity data set of 40 protein-RNA complexes, for which at least one unbound partner is available in the docking benchmark. The data set covers a wide affinity range of eight orders of magnitude as well as four different structural classes. On average, we find the complexes with single-stranded RNA have the highest affinity, whereas the complexes with the duplex RNA have the lowest. Nevertheless, free energy gain upon binding is the highest for the complexes with ribosomal proteins and the lowest for the complexes with tRNA with an average of -5.7 cal/mol/Å
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