ArticleJournal of chemical theory and computation2020
Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 95 citations in OpenAlex.
- Comparing Enhanced Sampling Methods in Exploring the Conformational Space of β-CateninThe journal of physical chemistry. B · 2026Article
- Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields.Journal of chemical information and modeling · 2026Article
- Molecular Dynamics-Instantaneous Frequencies of Molecules Method to Address the Performance of Classical and Rigid Water Force Fields.The journal of physical chemistry. B · 2026Article
- Investigating the electrostatics underlying activation of the βBiochimica et biophysica acta. Biomembranes · 2026Article
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Weighted Ensemble Simulations With the Drude Polarizable Model.Journal of computational chemistry · 2025Article
- A Simple, Polarizable, Rigid, 3-Point Water Model Using the Direct Polarization Approximation.Journal of chemical theory and computation · 2025Article
- Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.Journal of chemical theory and computation · 2025Article
- Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water.Journal of chemical theory and computation · 2025Article
- Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation.Journal of computational 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
- Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations.Macromolecules · 2025Article
- The interplay of polarizable water and protein in the activation of the M2 channel.Frontiers in pharmacology · 2025Article
- Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0].Living journal of computational molecular science · 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
- Small Molecule NS11021 Promotes BK Channel Activation by Increasing Inner Pore Hydration.Journal of chemical information and modeling · 2024Article
- Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer.The journal of physical chemistry. B · 2024Article
- Electronic Polarization Leads to a Drier Dewetted State for Hydrophobic Gating in the Big Potassium Channel.The journal of physical chemistry letters · 2024Article
- Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β-peptide.Proteins · 2024Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
The CHARMM Drude-2013 polarizable force field (FF) was developed to include the explicit treatment of induced electronic polarizability, resulting in a more accurate description of the electrostatic interactions in molecular dynamics (MD) simulations. While the Drude-2013 protein FF has shown success in improving the folding properties of α-helical peptides and to reproduce experimental observables in simulations up to 1 μs, some limitations were noted regarding the stability of β-sheet structures in simulations longer than 100 ns as well as larger deviations from crystal structures in simulations of a number of proteins compared to the additive CHARMM36 protein FF. The origin of the instability has been identified and appears to be primarily due to overestimated atomic polarizabilities and induced dipole-dipole interactions on the Cβ, Cγ, and Cδ side chain atoms. To resolve this and other issues, a number of aspects of the model were revisited, resulting in Drude-2019 protein FF. Backbone parameters were optimized targeting the conformational properties of the (Ala)
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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.