ArticleThe journal of physical chemistry. B2011
Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 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
- Perspective - RNA Dynamics Today and Tomorrow.Journal of molecular biology · 2026Review
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 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
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 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
- Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine.Nucleic acids research · 2025Article
- Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes.Journal of chemical theory and computation · 2024Article
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 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
- Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.Journal of chemical theory and computation · 2023Article
- Structure of pre-miR-31 reveals an active role in Dicer-TRBP complex processing.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.Journal of chemical information and modeling · 2023Article
- Structure of pre-miR-31 reveals an active role in Dicer processing.bioRxiv : the preprint server for biology · 2023Article
- Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA.Journal of molecular biology · 2022Article
- Review
- A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA.Journal of molecular modeling · 2021Article
- Structural basis for transcriptional start site control of HIV-1 RNA fate.Science (New York, N.Y.) · 2020Article
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5 authors.
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Abstract
Accurately modeling unpaired regions of RNA is important for predicting structure, dynamics, and thermodynamics of folded RNA. Comparisons between NMR data and molecular dynamics simulations provide a test of force fields used for modeling. Here, NMR spectroscopy, including NOESY, (1)H-(31)P HETCOR, DQF-COSY, and TOCSY, was used to determine conformational preferences for single-stranded GACC RNA. The spectra are consistent with a conformational ensemble containing major and minor A-form-like structures. In a series of 50 ns molecular dynamics (MD) simulations with the AMBER99 force field in explicit solvent, initial A-form-like structures rapidly evolve to disordered conformations. A set of 50 ns simulations with revised χ torsions (AMBER99χ force field) gives two primary conformations, consistent with the NMR spectra. A single 1.9 μs MD simulation with the AMBER99χ force field showed that the major and minor conformations are retained for almost 68% of the time in the first 700 ns, with multiple transformations from A-form to non-A-form conformations. For the rest of the simulation, random-coil structures and a stable non-A-form conformation inconsistent with NMR spectra were seen. Evidently, the AMBER99χ force field improves structural predictions for single-stranded GACC RNA compared to the AMBER99 force field, but further force field improvements are needed.
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