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 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 …

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 …

The field of data-driven chemistry is undergoing an evolution, driven by innovations in
machine learning models for predicting molecular properties and behavior. Recent strides in …

In the current drug development process, molecular dynamics (MD) simulations have proven
to be very useful. This chapter provides an overview of the current applications of MD …

The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of
any biological system and yet, many aspects of its role remain elusive. Here, we simulate …

Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation
via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. 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 …