ArticleNature communications2020
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
47 citing papers in PubMed, 82 citations in OpenAlex.
- Exploring Conformational Transitions of Adenine RNA Dimer via Machine Learning Potentials.Journal of chemical theory and computation · 2026Article
- Integrative in silico and in vitro screening of small molecules targeting RNA.Current protocols · 2026Article
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- Special Issue "Application of NMR Spectroscopy in Biomolecules".International journal of molecular sciences · 2026Article
- Decoding RNA Structural Ensembles: Energy Landscape Exploration of the TAR Stemloop.Journal of chemical theory and computation · 2026Article
- Covalent Probes Reveal Small-Molecule Binding Pockets in Structured RNA and Enable Bioactive Compound Design.Journal of the American Chemical Society · 2025Article
- Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.Molecules (Basel, Switzerland) · 2025Article
- Structure guided discovery of small molecule ligands targeting the oncomiR-1 NPSL2 hairpin.Scientific reports · 2025Article
- Article
- Ligand-binding pockets in RNA and where to find them.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function.Current opinion in structural biology · 2024Review
- Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (New York, N.Y.) · 2024Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Insights into the A-C Mismatch Conformational Ensemble in Duplex DNA and its Role in Genetic Processes through a Structure-based Review.Journal of molecular biology · 2024Review
- FRET-guided modeling of nucleic acids.Nucleic acids research · 2024Article
- Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent.Biophysical reviews · 2024Review
- Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix.bioRxiv : the preprint server for biology · 2024Article
- Hierarchical Assembly of Single-Stranded RNA.Journal of chemical theory and computation · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- sRNA Structural Modeling Based on NMR Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands of conformations far exceeds that of experimental measurements. We addressed this data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformation library. Refinement of this library with NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model accuracy was independently supported by comparisons to quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through designed ensemble redistribution via atomic mutagenesis. Applications to TAR bulge variants and more complex tertiary RNAs support the generality of this approach and the potential to make the determination of atomic-resolution RNA ensembles routine.
Indexed as
Identifiers
What OpenQuestion holds
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.