High-throughput molecular dynamics: the powerful new tool for drug discovery

► Molecular dynamics (MD) is able to provide quantitative insight into the kinetics of drug-ligand binding processes. ► MD cost substantially reduced by new developments in computing hardware. ► Markov state modelling using moves MD simulation from a high performance to high-throughput activity. ► High-throughput MD now a valuable tool in computational drug design. Molecular dynamics simulations are capable of resolving molecular recognition processes with chemical accuracy, but their practical application is popularly considered limited to the timescale accessible to a single simulation, which is far below biological timescales. In this perspective article, we propose that the true limiting factor for molecular dynamics is rather the high hardware and electrical power costs, which constrain not only the length of runs but also the number that can be performed concurrently. As a result of innovation in accelerator processors and high-throughput protocols, the cost of molecular dynamics sampling has been dramatically reduced and we argue that molecular dynamics simulation is now placed to become a key technology for in silico drug discovery in terms of binding pathways, poses, kinetics and affinities.