ReviewWiley interdisciplinary reviews. RNA2017
Physics-based all-atom modeling of RNA energetics and structure.
Review in Wiley interdisciplinary reviews. RNA, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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.
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Who cites it
21 citing papers in PubMed.
- Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities.bioRxiv : the preprint server for biology · 2026Article
- From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields.Journal of chemical theory and computation · 2026Article
- Kinetics, thermodynamics, and mechanisms of PMO interactions from computational molecular modeling.Molecular therapy. Nucleic acids · 2026Article
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking.Journal of chemical theory and computation · 2026Article
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.Biophysical journal · 2026Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.Journal of chemical theory and computation · 2023Article
- Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication*.Angewandte Chemie (International ed. in English) · 2021Article
- Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication.Angewandte Chemie (Weinheim an der Bergstrasse, Germany) · 2021Article
- Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations.Nucleic acids research · 2020Article
- In silico survey of the central conserved regions in viroids of theRNA (New York, N.Y.) · 2019Article
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Polarizable force field for RNA based on the classical drude oscillator.Journal of computational chemistry · 2018Article
- Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.Journal of chemical theory and computation · 2018Article
- Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.RNA (New York, N.Y.) · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422.
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Registered trials
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