ArticleProceedings of the National Academy of Sciences of the United States of America2019
Blind tests of RNA-protein binding affinity prediction.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
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- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Integrating FRET and Molecular Dynamics Simulation for Single-Molecule Aptameric Detection of Staphylococcus aureus IsdA Surface Protein.Biotechnology journal · 2025Article
- The RNA-binding protein RRP1 brakes macrophage one-carbon metabolism to suppress autoinflammation.Nature communications · 2025Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.Nucleic acids research · 2025Article
- Emerging roles of RNA binding proteins in intervertebral disc degeneration and osteoarthritis.Orthopaedic surgery · 2023Review
- RNA-Protein Interactome at the Hepatitis E Virus Internal Ribosome Entry Site.Microbiology spectrum · 2023Article
- Isolation of 5' regulatory region of3 Biotech · 2023Article
- CRISPRi-mediated tunable control of gene expression level with engineered single-guide RNA in Escherichia coli.Nucleic acids research · 2023Article
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- UPF1 mutants with intact ATPase but deficient helicase activities promote efficient nonsense-mediated mRNA decay.Nucleic acids research · 2022Article
- Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses.Journal of cheminformatics · 2022Article
- A Mathematical Analysis of HDV Genotypes: From Molecules to Cells.Mathematics (Basel, Switzerland) · 2021Article
- Mapping invisible epitopes by NMR spectroscopy.The Journal of biological chemistry · 2020Article
- Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures.PLoS computational biology · 2020Article
- On the Upper Bounds of the Real-Valued Predictions.Bioinformatics and biology insights · 2019Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Interactions between RNA and proteins are pervasive in biology, driving fundamental processes such as protein translation and participating in the regulation of gene expression. Modeling the energies of RNA-protein interactions is therefore critical for understanding and repurposing living systems but has been hindered by complexities unique to RNA-protein binding. Here, we bring together several advances to complete a calculation framework for RNA-protein binding affinities, including a unified free energy function for bound complexes, automated Rosetta modeling of mutations, and use of secondary structure-based energetic calculations to model unbound RNA states. The resulting Rosetta-Vienna RNP-ΔΔG method achieves root-mean-squared errors (RMSEs) of 1.3 kcal/mol on high-throughput MS2 coat protein-RNA measurements and 1.5 kcal/mol on an independent test set involving the signal recognition particle, human U1A, PUM1, and FOX-1. As a stringent test, the method achieves RMSE accuracy of 1.4 kcal/mol in blind predictions of hundreds of human PUM2-RNA relative binding affinities. Overall, these RMSE accuracies are significantly better than those attained by prior structure-based approaches applied to the same systems. Importantly, Rosetta-Vienna RNP-ΔΔG establishes a framework for further improvements in modeling RNA-protein binding that can be tested by prospective high-throughput measurements on new systems.
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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.