ArticleThe journal of physical chemistry. B2014
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.Journal of chemical theory and computation · 2024Article
- Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.Journal of chemical theory and computation · 2024Article
- A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.Journal of chemical theory and computation · 2024Article
- Polarizable AMOEBA Model for Simulating MgJournal of chemical information and modeling · 2024Article
- Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions.Journal of chemical information and modeling · 2022Article
- Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.The journal of physical chemistry. B · 2022Article
- Article
- Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.Journal of chemical theory and computation · 2022Article
- High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations.Langmuir : the ACS journal of surfaces and colloids · 2022Article
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
- Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.The journal of physical chemistry. B · 2022Article
- Cation competition and recruitment around the c-kit1 G-quadruplex using polarizable simulations.Biophysical journal · 2021Article
- Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations.Physical chemistry chemical physics : PCCP · 2021Article
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- Ion Binding Properties and Dynamics of theJournal of chemical information and modeling · 2020Article
- Contributions and competition of MgRNA (New York, N.Y.) · 2020Article
- Transferable interactions of LiThe Journal of chemical physics · 2020Article
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2 authors.
Funding
Abstract
Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems.
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