Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

The introduction of accelerator devices such as graphics processing units (GPUs) has had
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …

Membrane proteins have diverse functions within cells and are well-established drug
targets. The advances in membrane protein structural biology have revealed drug and lipid …

The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …

We report the implementation of the thermodynamic integration method on the pmemd
module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically …

Monoamine oxidases (MAOs), specifically MAO-A and MAO-B, play important roles in the
breakdown of monoamine neurotransmitters. Therefore, MAO inhibitors are crucial for …

Harnessing the power of graphics processing units (GPUs) to accelerate molecular
dynamics (MD) simulations in the context of free-energy calculations has been a …

Highlights•Free energy calculations and computational solvent analysis guiding drug
discovery.•Drug discovery programs targeting acetyl-CoA carboxylase and tyrosine kinase …

Introduction: Despite improved treatment options, colorectal cancer (CRC) remains a huge
public health concern with a significant impact on affected individuals. Cell cycle …

There has been a resurgence of interest in free energy methods motivated by the
performance enhancements offered by molecular dynamics (MD) software written for …