In silico tools, such as molecular docking, are widely applied to study interactions and
binding affinity of biological activity of proteins and peptides. However, restricted sampling of …

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …

Nowadays, hybrid QM/MM approaches are widely used to study (supra) molecular systems
embedded in complex biological matrices. However, in their common formulation, mutual …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

Classical molecular dynamics simulates the time evolution of molecular systems through the
phase space spanned by the positions and velocities of the constituent atoms. Molecular …

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 …

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

Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …

Changes in free energy provide valuable information for molecular recognition, including
both ligand–receptor binding thermodynamics and kinetics. Umbrella sampling (US), a …