ArticleScientific data2020
Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.
Article in Scientific data, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Estimating Permeabilities from Biased Molecular Dynamics with a Green-Kubo Formalism for Transport across the Blood-Brain Barrier.Journal of chemical information and modeling · 2026Article
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Navigating chemical space: multi-level Bayesian optimization with hierarchical coarse-graining.Chemical science · 2025Article
- A Coarse-Grained Molecular Dynamics Perspective on the Release of 5-Fluorouracil from Liposomes.Molecular pharmaceutics · 2024Article
- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery.Membranes · 2023Review
- Automatic Optimization of Lipid Models in the Martini Force Field UsingJournal of chemical information and modeling · 2023Article
- Recent advances on molecular dynamics-based techniques to address drug membrane permeability with atomistic detail.BBA advances · 2023Article
- Engineering of 2D nanomaterials to trap and kill SARS-CoV-2: a new insight from multi-microsecond atomistic simulations.Drug delivery and translational research · 2022Article
- Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design.Pharmaceuticals (Basel, Switzerland) · 2021Review
- The Bacteriostatic Activity of 2-Phenylethanol Derivatives Correlates with Membrane Binding Affinity.Membranes · 2021Article
- High-performance macromolecular data delivery and visualization for the web.Acta crystallographica. Section D, Structural biology · 2020Article
- Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.Scientific data · 2020Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes-exhaustively enumerating all 105 CG dimers-and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.
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