ArticleNature communications2021
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Spectral Graph Features for Reference-free RNA 3D Quality Assessment.bioRxiv : the preprint server for biology · 2026Article
- Could statistical potential models achieve comparable or better performance than deep learning models?Briefings in bioinformatics · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.PLoS biology · 2026Article
- Article
- Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps.Communications biology · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Article
- Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.Proteins · 2026Article
- On the Completeness of Existing RNA Fragment Structures.Genomics, proteomics & bioinformatics · 2025Article
- IRESeek: structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs.NAR genomics and bioinformatics · 2025Article
- RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.Scientific reports · 2025Article
- RNAtive to recognize native-like structure in a set of RNA 3D models.Bioinformatics (Oxford, England) · 2025Article
- Generative AI for computational chemistry: A roadmap to predicting emergent phenomena.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Review
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Refining modelled structures to approach experimental accuracy is one of the most challenging problems in molecular biology. Despite many years' efforts, the progress in protein or RNA structure refinement has been slow because the global minimum given by the energy scores is not at the experimentally determined "native" structure. Here, we propose a fully knowledge-based energy function that captures the full orientation dependence of base-base, base-oxygen and oxygen-oxygen interactions with the RNA backbone modelled by rotameric states and internal energies. A total of 4000 quantum-mechanical calculations were performed to reweight base-base statistical potentials for minimizing possible effects of indirect interactions. The resulting BRiQ knowledge-based potential, equipped with a nucleobase-centric sampling algorithm, provides a robust improvement in refining near-native RNA models generated by a wide variety of modelling techniques.
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