ArticleThe journal of physical chemistry. B2011
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.
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 55 papers.
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Who cites it
55 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
- Lessons Learned on Obtaining Reliable Dynamic Properties for Ionic Liquids.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field.The journal of physical chemistry letters · 2025Article
- The interplay of polarizable water and protein in the activation of the M2 channel.Frontiers in pharmacology · 2025Article
- Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics.Journal of chemical theory and computation · 2024Article
- Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Updates to Protex for Simulating Proton Transfers in an Ionic Liquid.The journal of physical chemistry. B · 2024Article
- Modeling Substrate Entry into the P-Glycoprotein Efflux Pump at the Blood-Brain Barrier.Journal of medicinal chemistry · 2023Article
- Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.Journal of chemical theory and computation · 2023Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.Journal of chemical theory and computation · 2022Article
- Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.The journal of physical chemistry. B · 2022Article
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.Journal of computational chemistry · 2020Article
- Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.Chemical reviews · 2019Review
- Polarizable force field for RNA based on the classical drude oscillator.Journal of computational chemistry · 2018Article
- Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with MgThe journal of physical chemistry. A · 2018Article
- CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.Journal of chemical theory and computation · 2018Article
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3 authors.
Funding
Abstract
A polarizable force field for nucleic acid bases based on the classical Drude oscillator model is presented. Parameter optimization was performed to reproduce crystallographic geometries, crystal unit cell parameters, heats of sublimation, vibrational frequencies and assignments, dipole moments, molecular polarizabilities and quantum mechanical base-base and base-water interaction energies. The training and validation data included crystals of unsubstituted and alkyl-substituted adenine, guanine, cytosine, uracil, and thymine bases, hydrated crystals, and hydrogen bonded base pairs. Across all compounds, the RMSD in the calculated heats of sublimation is 4.1%. This equates to an improvement of more than 2.5 kcal/mol in accuracy compared to the nonpolarizable CHARMM27 force field. However, the level of agreement with experimental molecular volume decreased from 1.7% to 2.1% upon moving from the nonpolarizable to the polarizable model. The representation of dipole moments is significantly improved with the Drude polarizable force field. Unlike in additive force fields, there is no requirement for the gas-phase dipole moments to be overestimated, illustrating the ability of the Drude polarizable force field to treat accurately differently dielectric environments and indicating the improvements in the electrostatic model. Validation of the model was performed on the basis of the calculation of the gas-phase binding enthalpies of base pairs obtained via potential of mean force calculations; the additive and polarizable models both performed satisfactorily with average differences of 0.2 and 0.9 kcal/mol, respectively, and rms differences of 1.3 and 1.7 kcal/mol, respectively. Overall, considering the number of significant improvements versus the additive CHARMM force field, the incorporation of explicit polarizability into the force field for nucleic acid bases represents an additional step toward accurate computational modeling of biological systems.
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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.