ArticleJournal of chemical theory and computation2011
Evaluation of DNA Force Fields in Implicit Solvation.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.The journal of physical chemistry. B · 2022Article
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- Article
- The "sugar" coarse-grained DNA model.Journal of molecular modeling · 2017Article
- Protocols for Molecular Dynamics Simulations of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.PloS one · 2016Article
- Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.Journal of chemical theory and computation · 2015Article
- Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations.Journal of chemical information and modeling · 2014Article
- Design and application of implicit solvent models in biomolecular simulations.Current opinion in structural biology · 2014Review
- Twenty-five years of nucleic acid simulations.Biopolymers · 2013Article
- A novel implicit solvent model for simulating the molecular dynamics of RNA.Biophysical journal · 2013Article
- Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.Journal of chemical theory and computation · 2013Article
- Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.Journal of chemical theory and computation · 2012Article
- Molecular modeling of nucleic acid structure: setup and analysis.Current protocols in nucleic acid chemistry · 2001Article
- Molecular modeling of nucleic acid structure: electrostatics and solvation.Current protocols in nucleic acid chemistry · 2001Article
- Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
2 authors.
Funding
Abstract
DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models.
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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.