Bio-molecular dynamics (MD) simulations based on graphical processing units (GPUs)
were first released to the public in the early 2009 with the code ACEMD. Almost 8 years after, applications
now encompass a broad range of molecular studies, while throughput improvements have
opened the way to millisecond sampling timescales. Based on an extrapolation of the amount of sampling
in published literature, the second timescale will be reached by the year 2022, and therefore we
predict that molecular dynamics is going to become one of the main tools in drug discovery in both
academia and industry. Here, we review successful applications in the drug discovery domain developed
over these recent years of GPU-based MD. We also retrospectively analyse limitations that have
been overcome over the years and give a perspective on challenges that remain to be addressed.
Keywords: Molecular dynamics, Simulation, Drug discovery, ACEMD, Perspective, Review, GPU.
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