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 …

Metadynamics is a popular enhanced sampling algorithm for computing the free energy
landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary …

The study of the rare transitions that take place between long lived metastable states is a
major challenge in molecular dynamics simulations. Many of the methods suggested to …

The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …

Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …

The prediction of drug–target binding and unbinding kinetics that occur on time scales
between milliseconds and several hours is a prime challenge for biased molecular …

Studying the pathways of ligand–receptor binding is essential to understand the mechanism
of target recognition by small molecules. The binding free energy and kinetics of protein …

The effect of an externally applied directional force on molecular friction is so far poorly
understood. Here, we study the force-driven dissociation of the ligand-protein complex biotin …

Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in
order to allow the description of processes occurring on biologically relevant timescales. For …

Exploration of the chemical reaction space of chemical transformations in multicomponent
mixtures is one of the main challenges in contemporary computational chemistry. To remove …