Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in
agricultural byproduct valorization and high-activity peptide screening. The introduction of …

Designing a reliable computational methodology to calculate protein: ligand standard
binding free energies is extremely challenging. The large change in configurational enthalpy …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

Virtual screening (VS) is an outstanding cornerstone in the drug discovery pipeline. A variety
of computational approaches, which are generally classified as ligand-based (LB) and …

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …

Free-energy calculations have seen increased usage in structure-based drug design.
Despite the rising interest, automation of the complex calculations and subsequent analysis …

Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

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 …

Conspectus The observation of complex structural transitions in biological and abiological
molecular objects within time scales amenable to molecular dynamics (MD) simulations is …

Absolute binding free energy calculations with explicit solvent molecular simulations can
provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to …