ArticleJournal of chemical theory and computation2022
Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies.Molecular therapy. Nucleic acids · 2024Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.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
- Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.Journal of chemical theory and computation · 2023Article
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
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Authors and funding
4 authors.
Funding
Abstract
RNA is a key participant in many biological processes, but studies of RNA using computer simulations lag behind those of proteins, largely due to less-developed force fields and the slow dynamics of RNA. Generating converged RNA ensembles for force field development and other studies remains a challenge. In this study, we explore the ability of replica exchange molecular dynamics to obtain well-converged conformational ensembles for two RNA hairpin systems in an implicit solvent. Even for these small model systems, standard REMD remains computationally costly, but coupling to a pre-generated structure library using the reservoir REMD approach provides a dramatic acceleration of ensemble convergence for both model systems. Such precise ensembles could facilitate RNA force field development and validation and applications of simulation to more complex RNA systems. The advantages and remaining challenges of applying R-REMD to RNA are investigated in detail.
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