ReviewProceedings of the National Academy of Sciences of the United States of America2013
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations.
Review in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 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
127 citing papers in PubMed.
- Recovering Small Molecule Ligand-RNA Binding Pocket Binding Modes and Exploring Potential Binding Pathways Using Metadynamics.Molecules (Basel, Switzerland) · 2026Article
- From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields.Journal of chemical theory and computation · 2026Article
- Perspective - RNA Dynamics Today and Tomorrow.Journal of molecular 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
- Modified Polycyclic Compounds Rescue Mis-splicing in Myotonic Dystrophy Type 1 Disease Models.ACS chemical biology · 2026Article
- NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.Biophysical journal · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- DynaRNA: accurate dynamic RNA conformation ensemble generation with diffusion model.Communications biology · 2025Article
- RNA adapts its flexibility to efficiently fold and resist unfolding.Nucleic acids research · 2025Article
- Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy.Nucleic acids research · 2025Article
- 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
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme.Nucleic acids research · 2024Article
- The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch.Nucleic acids research · 2024Article
- Inosine-Induced Base Pairing Diversity during Reverse Transcription.ACS chemical biology · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers.Molecular therapy. Nucleic acids · 2023Article
- Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.Journal of chemical theory and computation · 2023Article
67 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
We report the de novo folding of three hyperstable RNA tetraloops to 1-3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations.
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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.