Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

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 …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Cationic agents, such as ionic liquids (ILs)-based species, have broad-spectrum
antibacterial activities. However, the antibacterial mechanisms lack systematic and …

For simulations of membranes and membrane proteins, the generation of the lipid bilayer is
a critical step in the setup of the system. Membranes comprising multiple components pose …

Molecular dynamics simulations require barostats to be performed at a constant pressure.
The usual recipe is to employ the Berendsen barostat first, which displays a first-order …

The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …

Coarse-grained molecular dynamics provides a means for simulating the assembly and
interactions of macromolecular complexes at a reduced level of representation, thereby …

To efficiently insert a protein into an equilibrated and fully hydrated membrane with minimal
membrane perturbation we present a computational tool, called g_membed, which is part of …

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular
mechanisms whereby they fulfill these functions requires detailed biophysical and structural …