ReviewChemical reviews2018
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Review in Chemical reviews, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 279 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.
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Who cites it
279 citing papers in PubMed, 633 citations in OpenAlex.
- Article
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Kinetics, thermodynamics, and mechanisms of PMO interactions from computational molecular modeling.Molecular therapy. Nucleic acids · 2026Article
- Exploring Conformational Transitions of Adenine RNA Dimer via Machine Learning Potentials.Journal of chemical theory and computation · 2026Article
- From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields.Journal of chemical theory and computation · 2026Article
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Perspective - RNA Dynamics Today and Tomorrow.Journal of molecular biology · 2026Review
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- A magic methyl effect in the active site of a methyltransferase ribozyme.Nature communications · 2026Article
- Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot With Thermodynamics-Driven Machine Learning.Journal of computational chemistry · 2026Article
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.Current opinion in structural biology · 2026Review
- 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
- Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1.Journal of chemical information and modeling · 2026Article
- Beyond the Sequence: Chemical and Topological Design and Innovations in mRNA Therapeutics.Chemical reviews · 2026Review
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
219 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 5 institutions in 4 countries.
Funding
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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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.