Determining the presence of water molecules at protein–ligand
interfaces is still a challenging task in free-energy calculations.
The inappropriate placement of water molecules results in the stabilization
of wrong conformational orientations of the ligand. With classical
alchemical perturbation methods, such as thermodynamic integration
(TI), it is essential to know the amount of water molecules in the
active site of the respective ligands. However, the resolution of
the crystal structure and the correct assignment of the electron density
do not always lead to a clear placement of water molecules. In this
work, we apply the one-step perturbation method named accelerated
enveloping distribution sampling (AEDS) to determine the presence
of water molecules in the active site by probing them in a fast and
straightforward way. Based on these results, we combined the AEDS
method with standard TI to calculate accurate binding free energies
in the presence of buried water molecules. The main idea is to perturb
the water molecules with AEDS such that they are allowed to alternate
between regular water molecules and non-interacting dummy particles
while treating the ligand with TI over an alchemical pathway. We demonstrate
the use of AEDS to probe the presence of water molecules for six different
test systems. For one of these, previous calculations showed difficulties
to reproduce the experimental binding free energies, and here, we
use the combined TI–AEDS approach to tackle these issues.