ArticleJournal of chemical theory and computation2010
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 199 papers.
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Who cites it
199 citing papers in PubMed.
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- 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
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- Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.bioRxiv : the preprint server for biology · 2026Article
- Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking.Journal of chemical theory and computation · 2026Article
- Programmable kinetic barcoding for multiplexed RNA detection with Cas13a.Nature biomedical engineering · 2026Article
- Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning.Nature biotechnology · 2026Article
- Decoding RNA Structural Ensembles: Energy Landscape Exploration of the TAR Stemloop.Journal of chemical theory and computation · 2026Article
- Potential for gene silencing by piwi-interacting RNA in three lepidopterans.Frontiers in insect science · 2026Article
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- Conformational changes induced by K949A mutation in the CRISPR-Cas12a complex drives an effective target-binding mechanism.Current research in structural biology · 2025Article
- Success and Limitations of Current Force Fields for the Description of RNA-Ligand Complexes.The journal of physical chemistry. B · 2025Article
- Molecular drivers of RNA phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Mutational scanning of TnpB reveals latent activity for genome editing.bioRxiv : the preprint server for biology · 2025Article
- CRISPR-Cas12a REC2-Nuc interactions drive target-strand cleavage and constrain trans cleavage.Nucleic acids research · 2025Article
139 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5'-UNCG-3' and 5'-GNRA-3' RNA tetraloops are the most important classes of RNA hairpin loops. Both tetraloops are highly structured with characteristic signature three-dimensional features and are recurrently seen in functional RNAs and ribonucleoprotein particles. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, the outcome of simulations is often compromised by imperfections in the parametrization of simplified pairwise additive empirical potentials referred to also as force fields. We have pointed out in several recent studies that a force field description of single-stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. First, we utilized the three widely used variants of Cornell et al. (AMBER) force fields known as
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