ArticleJournal of chemical information and modeling2016
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.
Article in Journal of chemical information and modeling, 2016. 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
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Who cites it
94 citing papers in PubMed, 223 citations in OpenAlex.
- 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
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- Molecular Dynamics Simulation of Passive Diffusion across a Human Breast Cancer Cell Membrane Model. Comparison between Cisplatin and Its Pt(IV) Derivatives.Journal of chemical information and modeling · 2026Article
- Review
- Quantifying Membrane Structure and Dynamics during Bioproduct Production inThe journal of physical chemistry. B · 2026Article
- Intracellular accumulation of hydrophobic 1,3-PDN inhibits methanogenesis in rumen methanogens.The ISME journal · 2026Article
- Impact of Lipid Composition on Membrane Partitioning and Permeability of Gas Molecules.Membranes · 2026Article
- Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment.The journal of physical chemistry. B · 2025Article
- Probing Passive Permeation of Tetracycline: Are Simulations Ready for beyond-Rule-of-Five Drug Permeability Calculation?The journal of physical chemistry. B · 2025Article
- Computational design of an improved photoswitchable psychedelic based on light absorption, membrane permeation and protein binding.Physical chemistry chemical physics : PCCP · 2025Article
- Presence of Different Ceramide Species Modulates Barrier Function and Structure of Stratum Corneum Lipid Membranes: Insights from Molecular Dynamics Simulations.Molecular pharmaceutics · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Prodrug Approach as a Strategy to Enhance Drug Permeability.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Permeability Benchmarking: Guidelines for ComparingJournal of chemical information and modeling · 2025Review
- Establishing a General Atomistic Model for the Stratum Corneum Lipid Matrix Based on Experimental Data for Skin Permeation Studies.International journal of molecular sciences · 2025Article
- Article
- Elucidating Antibiotic Permeation through theJournal of chemical information and modeling · 2024Article
- Tunneling Mechanisms of Quinones in Photosynthetic Reaction Center-Light Harvesting 1 Supercomplexes.Small science · 2024Article
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Investigation of the Anti-Inflammatory Properties of Bioactive Compounds fromMolecules (Basel, Switzerland) · 2024Article
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
12 authors at 8 institutions in 4 countries.
Funding
Abstract
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient Pm was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized Langevin method, both being sensitive to chosen parameters and the slow relaxation of membrane defects. Agreement within 1.5 log units of the computed Pm with experiment is found for all permeants and methods. Remaining discrepancies can likely be attributed to limitations of the force field as well as slowly relaxing collective movements within the lipid environment. Numerical calculations based on model profiles show that Pm can be reliably estimated from only a few data points, leading to recommendations for calculating Pm from simulations.
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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.