Rigorous binding free energy methods in drug discovery are growing in popularity because
of a combination of methodological advances, improvements in computer hardware, and …

Recognizing the recent developments and applications of free energy methods, the Journal
of Chemical Information and Modeling extended an open invitation to the computational …

The accurate prediction of absolute protein–ligand binding free energies is one of the grand
challenge problems of computational science. Binding free energy measures the strength of …

Water is frequently found inside proteins, carrying out important roles in catalytic reactions or
molecular recognition tasks. Therefore, computational models that aim to study protein …

The ability to reliably compute accurate protein− ligand binding affinities is crucial to
understanding protein− ligand recognition and to structure-based drug design. A ligand's …

Binding free energy calculations offer a thermodynamically rigorous method to compute
protein–ligand binding, and they depend on empirical force fields with hundreds of …

One of the most important biological processes at the molecular level is the formation of
protein–ligand complexes. Therefore, determining their structure and underlying key …

Localized water molecules in the binding pockets of proteins play an important role in
noncovalent association of proteins and small drug compounds. At times, the dominant …

Computational methods, namely molecular dynamics (MD) simulations in combination with
inhomogeneous fluid solvation theory (IFST) were used to retrospectively investigate various …

Water molecules are commonplace in protein binding pockets, where they can typically form
a complex between the protein and a ligand or become displaced upon ligand binding. As a …