A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …

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 …

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 …

Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …

Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …

We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …

The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …

Driven by illicit fentanyl, opioid related deaths have reached the highest level in 2020.
Currently, an opioid overdose is resuscitated by the use of naloxone, which competitively …

Calculating the standard binding free energies of protein–protein and protein–ligand
complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of …

The ability to predict the intricate mechanistic behavior of ligands and associated structural
determinants during protein–ligand (un) binding is of great practical importance in drug …