ArticleThe journal of physical chemistry. B2015
CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 46 citations in OpenAlex.
- Mining lysine post-translational modification sites by integrating protein language model representations with structural context.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Development of AMOEBA Polarizable Force Field for Rare-Earth LaThe journal of physical chemistry. B · 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
- Automation of AMOEBA polarizable force field for small molecules: Poltype 2.Journal of computational chemistry · 2022Article
- Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- 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
- Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.Journal of computational chemistry · 2020Article
- Atomic partial charge predictions for furanoses by random forest regression with atom type symmetry function.RSC advances · 2020Article
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Polarizable force field for RNA based on the classical drude oscillator.Journal of computational chemistry · 2018Article
- CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.Journal of chemical theory and computation · 2018Article
- Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.Journal of chemical information and modeling · 2018Article
- Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.Carbohydrate research · 2018Article
- Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.Journal of chemical theory and computation · 2017Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
An empirical all-atom CHARMM polarizable force filed for aldopentofuranoses and methyl-aldopentofuranosides based on the classical Drude oscillator is presented. A single electrostatic model is developed for eight different diastereoisomers of aldopentofuranoses by optimizing the existing electrostatic and bonded parameters as transferred from ethers, alcohols, and hexopyranoses to reproduce quantum mechanical (QM) dipole moments, furanose-water interaction energies and conformational energies. Optimization of selected electrostatic and dihedral parameters was performed to generate a model for methyl-aldopentofuranosides. Accuracy of the model was tested by reproducing experimental data for crystal intramolecular geometries and lattice unit cell parameters, aqueous phase densities, and ring pucker and exocyclic rotamer populations as obtained from NMR experiments. In most cases the model is found to reproduce both QM data and experimental observables in an excellent manner, whereas for the remainder the level of agreement is in the satisfactory regimen. In aqueous phase simulations the monosaccharides have significantly enhanced dipoles as compared to the gas phase. The final model from this study is transferrable for future studies on carbohydrates and can be used with the existing CHARMM Drude polarizable force field for biomolecules.
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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.