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 …

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 …

Binding kinetic parameters can be correlated with drug efficacy, which in recent years led to
the development of various computational methods for predicting binding kinetic rates and …

While most work on the quantum simulation of chemistry has focused on computing energy
surfaces, a similarly important application requiring subtly different algorithms is the …

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 …

Progress in technology and algorithms throughout the past decade has transformed the field
of protein design and engineering. Computational approaches have become well-engrained …

Simulations with adaptive time-dependent bias enable an efficient exploration of the
conformational space of a system. However, the dynamic information is altered by the bias …

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 …

The dissociation of ligands from proteins and other biomacromolecules occurs over a wide
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …

Target residence time plays a crucial role in the pharmacological activity of small molecule
inhibitors. Little is known, however, about the underlying causes of inhibitor residence time …