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 traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

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 …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study
protein structure-related questions. Starting from the early simulation study on the …

This paper reviews various enhanced conformational sampling methods and explicit/implicit
solvent/membrane models, as well as their recent applications to the exploration of the …

Molecular dynamics simulations have emerged as a powerful tool to study biological
systems at varied length and timescales. The conventional all-atom molecular dynamics …

A coarse-grained (CG) model for peptides and proteins was developed as an extension of
the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was …

Simulations of membrane proteins have been rising in popularity in the past decade.
Advancements in technology and force fields made it possible to simulate behavior of …

The architecture of biological membranes is tightly coupled to the localization, organization,
and function of membrane proteins. The organelle-specific distribution of lipids allows for the …