[PDF][PDF] MembraneAnalysis. jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes

A Hossein, AJ Sodt - Journal of Open Source Software, 2023 - joss.theoj.org
Biological membranes separate living cells from their surroundings, and, in case of
eukaryotes, partition the cell into its constituent organelles. These bilayer structures, which …

[HTML][HTML] MOSAICS: A software suite for analysis of membrane structure and dynamics in simulated trajectories

N Bernhardt, JD Faraldo-Gómez - Biophysical Journal, 2023 - cell.com
Molecular dynamics (MD) simulations have become the predominant computational
analysis method in membrane biophysics, as this technique is uniquely suited for …

FATSLiM: a fast and robust software to analyze MD simulations of membranes

S Buchoux - Bioinformatics, 2017 - academic.oup.com
When studying biological membranes, Molecular Dynamics (MD) simulations reveal to be
quite complementary to experimental techniques. Because the simulated systems keep …

[HTML][HTML] Unraveling membrane properties at the organelle-level with LipidDyn

S Scrima, M Tiberti, A Campo… - Computational and …, 2022 - Elsevier
Cellular membranes are formed from different lipids in various amounts and proportions
depending on the subcellular localization. The lipid composition of membranes is sensitive …

[HTML][HTML] Efficient preparation and analysis of membrane and membrane protein systems

M Javanainen, H Martinez-Seara - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Molecular dynamics (MD) simulations have become a highly important technique to
consider lipid membrane systems, and quite often they provide considerable added value to …

MEMBPLUGIN: studying membrane complexity in VMD

R Guixà-González, I Rodriguez-Espigares… - …, 2014 - academic.oup.com
Computer simulations are giving way to more complex and accurate studies of biological
membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories …

[PDF][PDF] Lipid membranes: Theory and simulations bridged to experiments

I Vattulainen, T Róg - Biochim. Biophys. Acta, 2016 - helda.helsinki.fi
There are essentially five classes of molecules that are the corner stones of life. DNA in
terms of nucleic acids contains the information of building proteins that are the nanoscale …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

APL@ voro—interactive visualization and analysis of cell membrane simulations

M Kern, S Jaeger-Honz, F Schreiber, B Sommer - Bioinformatics, 2023 - academic.oup.com
Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of
complex processes such as changing membrane dynamics, lipid rafts and the …

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

SW Leong, TS Lim, YS Choong - Bioinforma.-Updat. Featur. Appl, 2016 - books.google.com
Biological membranes are complex environments consisting of different types of lipids and
membrane proteins. The structure of a lipid bilayer is typically difficult to study because the …