ArticleJournal of chemical theory and computation2016
Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Exploring Conformational Transitions of Adenine RNA Dimer via Machine Learning Potentials.Journal of chemical theory and computation · 2026Article
- Systematic modification of functionality in disordered elastic networks through free energy surface tailoring.Science advances · 2023Article
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.Journal of chemical theory and computation · 2022Article
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
- Development and Testing of the OPLS-AA/M Force Field for RNA.Journal of chemical theory and computation · 2019Article
- Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.Science advances · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.Journal of chemical theory and computation · 2018Article
- RNA force field with accuracy comparable to state-of-the-art protein force fields.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017Review
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- Unraveling MgRNA (New York, N.Y.) · 2017Article
- Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.Journal of chemical theory and computation · 2017Article
- Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.Journal of chemical theory and computation · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement.
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