ArticleFaraday discussions2014
Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
Article in Faraday discussions, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed.
- Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity.Science advances · 2025Article
- Dynamics and activation of membrane-bound B cell receptor assembly.Communications biology · 2025Article
- Dynamics and Activation of Membrane-Bound B Cell Receptor Assembly.bioRxiv : the preprint server for biology · 2024Article
- Electron videography of a lipid-protein tango.Science advances · 2024Article
- The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes.Chemical science · 2024Review
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- A brief history of visualizing membrane systems in molecular dynamics simulations.Frontiers in bioinformatics · 2023Article
- Adherens junctions organize size-selective proteolytic hotspots critical for Notch signalling.Nature cell biology · 2022Article
- Design - a new way to look at old molecules.Journal of integrative bioinformatics · 2022Article
- Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.Scientific reports · 2019Article
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- Influence of membrane lipid composition on the structure and activity of γ-secretase.Physical chemistry chemical physics : PCCP · 2018Article
- Computational Lipidomics of the Neuronal Plasma Membrane.Biophysical journal · 2017Article
- Article
- Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.Current opinion in structural biology · 2016Review
- Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane.The journal of physical chemistry. B · 2016Article
- Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes.The Journal of chemical physics · 2015Article
- Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.Biophysical journal · 2015Review
- Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.Journal of chemical theory and computation · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.
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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.