ArticleJournal of computer-aided molecular design2013
Computational analysis of local membrane properties.
Article in Journal of computer-aided molecular design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed, 183 citations in OpenAlex.
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- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Conformational Signatures of Preassembled and Active Complexes of 5-HTJournal of chemical information and modeling · 2025Article
- Cholesterol-dependent dimerization and conformational dynamics of EphA2 receptors from coarse-grained and all-atom simulations.Structure (London, England : 1993) · 2025Article
- Lipid Scrambling Pathways in the Sec61 Translocon Complex.Journal of the American Chemical Society · 2025Article
- Saddle curvature association of nsP1 facilitates the replication complex assembly of Chikungunya virus in cells.Nature communications · 2025Article
- Bayesian Nonparametric Analysis of Residence Times for Protein-Lipid Interactions in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- Any1 is a phospholipid scramblase involved in endosome biogenesis.The Journal of cell biology · 2025Article
- Distinct effects of progesterone and cholesterol on lipid membranes: insights from biophysical experiments and molecular dynamics simulations.Frontiers in molecular biosciences · 2025Article
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- Molecular and energetic analysis of the interaction and specificity of Maximin 3 with lipid membranes: In vitro and in silico assessments.Protein science : a publication of the Protein Society · 2024Article
- Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields.The journal of physical chemistry. B · 2024Article
- DPPA as a Potential Cell Membrane Component Responsible for Binding Amyloidogenic Protein Human Cystatin C.Molecules (Basel, Switzerland) · 2024Article
- Curvature Footprints of Transmembrane Proteins in Simulations with the Martini Force Field.The journal of physical chemistry. B · 2024Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the field of biomolecular simulations, dynamics of phospholipid membranes is of special interest. A number of proteins, including channels, transporters, receptors and short peptides are embedded in lipid bilayers and tightly interact with phospholipids. While the experimental measurements report on the spatial and/or temporal average membrane properties, simulation results are not restricted to the average properties. In the current study, we present a collection of methods for an efficient local membrane property calculation, comprising bilayer thickness, area per lipid, deuterium order parameters, Gaussian and mean curvature. The local membrane property calculation allows for a direct mapping of the membrane features, which subsequently can be used for further analysis and visualization of the processes of interest. The main features of the described methods are highlighted in a number of membrane systems, namely: a pure dimyristoyl-phosphatidyl-choline (DMPC) bilayer, a fusion peptide interacting with a membrane, voltage-dependent anion channel protein embedded in a DMPC bilayer, cholesterol enriched bilayer and a coarse grained simulation of a curved palmitoyl-oleoyl-phosphatidyl-choline lipid membrane. The local membrane property analysis proves to provide an intuitive and detailed view on the observables that are otherwise interpreted as averaged bilayer properties.
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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.