More than a half century ago it became feasible to simulate, using classical-mechanical
equations of motion, the dynamics of molecular systems on a computer. Since then classical …

Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …

Alchemical absolute binding free energy (ABFE) calculations have substantial potential in
drug discovery, but are often prohibitively computationally expensive. To unlock their …

As a contribution to the understanding and rationalization of methodological and modeling
effects in recent host–guest SAMPL challenges, using an alchemical molecular dynamics …

The majority of drug-like molecules contain at least one ionizable group, and many common
drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a …

Accurate prediction of the difference in binding free energy between compounds is crucial
for reducing the high costs associated with drug discovery. Relative binding free energy …

Polyphosphate nucleotides, such as ATP, ADP, GTP, and GDP, play a crucial role in
modulating protein functions through binding and/or catalytically activating proteins …

The confinement method is a reaction coordinate-free enhanced sampling method for the
calculation of conformational free energy differences. We show that in explicit solvent …

Under the influence of a temperature gradient, particles diffuse to their more favourable
temperature, inducing a concentration gradient that opposes Fickian diffusion, a …