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 …
Computational modeling of realistic cell membranes
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 …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Backmapping 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 …
Triglyceride lipolysis triggers liquid crystalline phases in lipid droplets and alters the LD proteome
Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs), but how
these lipids are organized within LDs and influence their proteome remain unclear. Using in …
these lipids are organized within LDs and influence their proteome remain unclear. Using in …
Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure
V Zoni, R Khaddaj, I Lukmantara… - Proceedings of the …, 2021 - National Acad Sciences
Lipid droplets (LDs) are intracellular organelles responsible for lipid storage, and they
emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly …
emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly …
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Residue-level coarse-grained (CG) models have become one of the most popular tools in
biomolecular simulations in the trade-off between modeling accuracy and computational …
biomolecular simulations in the trade-off between modeling accuracy and computational …
[HTML][HTML] Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity
In the last decade, molecular dynamics (MD) simulations have become an essential tool to
investigate the molecular properties of membrane trafficking processes, often in conjunction …
investigate the molecular properties of membrane trafficking processes, often in conjunction …
The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
The different combinations of molecular dynamics simulations with coarse-grained
representations have acquired considerable popularity among the scientific community …
representations have acquired considerable popularity among the scientific community …
Molecular dynamics simulations in photosynthesis
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments,
lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics …
lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics …