ArticleThe journal of physical chemistry. B2013
A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
94 citing papers in PubMed, 187 citations in OpenAlex.
- Computer-Aided Drug Design for Type 2 Diabetes-Related Enzymes: SILCS-Based Fragment Mapping, Pharmacophore Modeling, and Virtual Screening.Journal of chemical information and modeling · 2026Article
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Drude polarizable force field for phosphorylated polypeptides and proteins.Biophysical journal · 2026Article
- Investigating the electrostatics underlying activation of the βBiochimica et biophysica acta. Biomembranes · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- Weighted Ensemble Simulations With the Drude Polarizable Model.Journal of computational chemistry · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations.Macromolecules · 2025Article
- Do selectivity filter carbonyls in KJournal of structural biology: X · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer.The journal of physical chemistry. B · 2024Article
- Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β-peptide.Proteins · 2024Article
- Intrinsic Conformational Dynamics of Glycine and Alanine in Polarizable Molecular Dynamics Force Fields: Comparison to Spectroscopic Data.The journal of physical chemistry. B · 2024Article
- Water inside the Selectivity Filter of a KJournal of the American Chemical Society · 2024Article
- Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field.Journal of chemical theory and computation · 2023Article
- Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy.Journal of the American Chemical Society · 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
- Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.Journal of chemical information and modeling · 2023Article
- Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields.Physical chemistry chemical physics : PCCP · 2023Article
- Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein.Computational and structural biotechnology journal · 2023Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
A polarizable force field of saturated phosphatidylcholine-containing lipids based on the classical Drude oscillator model is optimized and used in molecular dynamics simulations of bilayer and monolayer membranes. The hierarchical parametrization strategy involves the optimization of parameters for small molecules representative of lipid functional groups, followed by their application in larger model compounds and full lipids. The polar headgroup is based on molecular ions tetramethyl ammonium and dimethyl phosphate, the esterified glycerol backbone is based on methyl acetate, and the aliphatic lipid hydrocarbon tails are based on linear alkanes. Parameters, optimized to best represent a collection of gas and liquid properties for these compounds, are assembled into a complete model of dipalmitoylphosphatidylcholine (DPPC) lipids that is tested against the experimental properties of bilayer and monolayer membranes. The polarizable model yields average structural properties that are in broad accord with experimental data. The area per lipid of the model is 60 Å(2), slightly smaller than the experimental value of 63 Å(2). The order parameters from nuclear magnetic resonance deuterium quadrupolar splitting measures, the electron density profile, and the monolayer dipole potential are in reasonable agreement with experimental data, and with the nonpolarizable CHARMM C36 lipid force field.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.