Molecular dynamics (MD) simulations are capable of reproducing dynamic evolution at the
molecular scale, but are limited by temporal scales. Enhanced sampling has emerged as a …

An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate
importance sampling in free energy simulations. The method achieves enhanced sampling …

The calculation of accurate free energies lies at the core of investigating biomolecular
processes such as protein− ligand binding, protein− antibody interactions, enzymatic …

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 …

Alchemical free-energy methods based on molecular dynamics (MD) simulations have
become important tools to identify modifications of small organic molecules that improve …

Relative binding free energy (RBFE) calculations have emerged as a powerful tool that
supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs …

Clostridium histolyticum is a Gram-positive anaerobic bacterium belonging to the
Clostridium genus. It produces collagenase, an enzyme involved in breaking down collagen …

Macromolecular recognition and ligand binding are at the core of biological function and
drug discovery efforts. Water molecules play a significant role in mediating the protein …

Replica-exchange envelo** distribution sampling (RE-EDS) is a pathway-independent
multistate free-energy method currently implemented in the GROMOS software package for …