ReviewThe journal of physical chemistry letters2014
Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model.
Review in The journal of physical chemistry letters, 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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67 citing papers in PubMed.
- Impact of Linker Defects on the Dielectric Properties of the Metal-Organic Framework HKUST-1: Insights from Molecular Dynamics Simulations.ACS applied materials & interfaces · 2026Article
- Enhancing Empirical Energy Functions Using Physics- and Machine Learning-Based Extensions: Structure, Dynamics and Spectroscopy of Modified Benzenes.Journal of computational chemistry · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation.Journal of computational chemistry · 2025Article
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClJournal of chemical theory and computation · 2025Article
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClbioRxiv : the preprint server for biology · 2024Article
- Article
- Chitosan Polysaccharides from a Polarizable Multiscale Approach.ACS omega · 2023Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 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
- Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin.Biophysical journal · 2023Article
- Computer-Aided Drug Design: An Update.Methods in molecular biology (Clifton, N.J.) · 2023Article
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber.Journal of chemical theory and computation · 2022Article
- Fast Polarizable Water Model for Atomistic Simulations.Journal of chemical theory and computation · 2022Article
- Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials.Journal of chemical information and modeling · 2022Article
- Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field.ACS physical chemistry Au · 2022Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- Progress in Simulation Studies of Insulin Structure and Function.Frontiers in endocrinology · 2022Review
- Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.Communications chemistry · 2022Review
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
7 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
In this Perspective, we summarize recent efforts to include the explicit treatment of induced electronic polarization in biomolecular force fields. Methods used to treat polarizability, including the induced dipole, fluctuating charge, and classical Drude oscillator models, are presented, including recent advances in force fields using those methods. This is followed by recent results obtained with the Drude model, including microsecond molecular dynamics (MD) simulations of multiple proteins in explicit solvent. Results show significant variability of backbone and side-chain dipole moments as a function of environment, including significant changes during individual simulations. Dipole moments of water in the vicinity of the proteins reveal small but systematic changes, with the direction of the changes dependent on the environment. Analyses of the full proteins show that the polarizable Drude model leads to larger values of the dielectric constant of the protein interior, especially in the case of hydrophobic regions. These results indicate that the inclusion of explicit electronic polarizability leads to significant differences in the physical forces affecting the structure and dynamics of proteins, which can be investigated in a computationally tractable fashion in the context of the Drude model.
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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.