ArticleJournal of computational chemistry2014
All-atom polarizable force field for DNA based on the classical Drude oscillator model.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes.Journal of chemical theory and computation · 2024Article
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field.Journal of chemical theory and computation · 2023Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
- Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.Journal of chemical information and modeling · 2023Article
- MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.Journal of computational chemistry · 2023Article
- Fast Polarizable Water Model for Atomistic Simulations.Journal of chemical theory and computation · 2022Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field.ACS physical chemistry Au · 2022Article
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
- 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
- A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA.Journal of molecular modeling · 2021Article
- Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.Journal of molecular modeling · 2020Article
- Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.Journal of chemical theory and computation · 2020Article
7 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Presented is a first generation atomistic force field (FF) for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages, and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive FF, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA.
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