Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …

Computational techniques have been applied in the drug discovery pipeline since the
1980s. Given the low computational resources of the time, the first molecular modeling …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

RNA-binding protein TDP-43 mediates essential RNA processing but forms cytoplasmic
neuronal inclusions via its C-terminal domain (CTD) in amyotrophic lateral sclerosis (ALS). It …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless
organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is …

Given the promising clinical value of allosteric modulators of G protein-coupled-receptors
(GPCRs), mechanistic understanding of how these modulators alter GPCR function is of …

Enhancing sampling and analyzing simulations are central issues in molecular simulation.
Recently, we introduced PLUMED, an open-source plug-in that provides some of the most …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …