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Two decades of Martini: Better beads, broader scope
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …
been around for nearly two decades. Originally developed for lipid‐based systems by the …
[HTML][HTML] Simulating realistic membrane shapes
Biological membranes exhibit diversity in their shapes and complexity in chemical
compositions that are linked to many cellular functions. These two central features of …
compositions that are linked to many cellular functions. These two central features of …
Backmap** triangulated surfaces to coarse-grained membrane models
Many biological processes involve large-scale changes in membrane shape. Computer
simulations of these processes are challenging since they occur across a wide range of …
simulations of these processes are challenging since they occur across a wide range of …
LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid
membranes with complex compositions. Here, we present LiPyphilic—a fast, fully tested …
membranes with complex compositions. Here, we present LiPyphilic—a fast, fully tested …
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that
modulates neuronal excitability, largely by allowing Ca2+ permeation. Agonist binding …
modulates neuronal excitability, largely by allowing Ca2+ permeation. Agonist binding …
Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological
membranes to carry out functions such as cell signalling, enzymatic activity, or membrane …
membranes to carry out functions such as cell signalling, enzymatic activity, or membrane …
Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models
We present a new technique for the rapid modeling and construction of scientifically
accurate mesoscale biological models. The resulting 3D models are based on a few 2D …
accurate mesoscale biological models. The resulting 3D models are based on a few 2D …
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries
In molecular simulations, periodic boundary conditions are typically used to avoid surface
effects occurring at the boundaries of the simulation box. A consequence of this is that …
effects occurring at the boundaries of the simulation box. A consequence of this is that …
Capturing biologically complex tissue-specific membranes at different levels of compositional complexity
Plasma membranes (PMs) contain hundreds of different lipid species that contribute
differently to overall bilayer properties. By modulation of these properties, membrane protein …
differently to overall bilayer properties. By modulation of these properties, membrane protein …
[HTML][HTML] Molecular dynamics simulations of curved lipid membranes
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma
membrane to the highly curved membranes of organelles, vesicles, and membrane …
membrane to the highly curved membranes of organelles, vesicles, and membrane …