Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023‏ - Wiley Online Library
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 …

[HTML][HTML] Simulating realistic membrane shapes

W Pezeshkian, SJ Marrink - Current opinion in cell biology, 2021‏ - Elsevier
Biological membranes exhibit diversity in their shapes and complexity in chemical
compositions that are linked to many cellular functions. These two central features of …

Backmap** triangulated surfaces to coarse-grained membrane models

W Pezeshkian, M König, TA Wassenaar… - Nature …, 2020‏ - nature.com
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 …

LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations

P Smith, CD Lorenz - Journal of chemical theory and computation, 2021‏ - ACS Publications
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 …

Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators

Y Zhuang, CM Noviello, RE Hibbs, RJ Howard… - Proceedings of the …, 2022‏ - pnas.org
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that
modulates neuronal excitability, largely by allowing Ca2+ permeation. Agonist binding …

Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?

AH Larsen, LH John, MSP Sansom… - Bioscience …, 2022‏ - portlandpress.com
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological
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

N Nguyen, O Strnad, T Klein, D Luo… - IEEE transactions on …, 2020‏ - ieeexplore.ieee.org
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 …

Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries

BMH Bruininks, TA Wassenaar… - Journal of chemical …, 2023‏ - ACS Publications
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 …

Capturing biologically complex tissue-specific membranes at different levels of compositional complexity

HI Ingólfsson, H Bhatia, T Zeppelin… - The Journal of …, 2020‏ - ACS Publications
Plasma membranes (PMs) contain hundreds of different lipid species that contribute
differently to overall bilayer properties. By modulation of these properties, membrane protein …

[HTML][HTML] Molecular dynamics simulations of curved lipid membranes

AH Larsen - International Journal of Molecular Sciences, 2022‏ - mdpi.com
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma
membrane to the highly curved membranes of organelles, vesicles, and membrane …