Drug‐binding kinetics could play important roles in determining the efficacy of drugs and has
caught the attention of more drug designers. Using the dissociation of 1H‐pyrrolo [2, 3‐b] …

Free energy calculations are rapidly becoming indispensable in structure-enabled drug
discovery programs. As new methods, force fields, and implementations are developed …

The accurate calculation of the binding free energy for arbitrary ligand–protein pairs is a
considerable challenge in computer-aided drug discovery. Recently, it has been …

Calculating the standard binding free energies of protein–protein and protein–ligand
complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of …

Accurate evaluation of protein–ligand binding free energies in silico is of paramount
importance for understanding the mechanisms of biological regulation and providing a …

The current status of reactive molecular dynamics (MD) simulations is summarized. Both,
methodological aspects and applications to problems ranging from gas phase reaction …

Many limitations of current computer-aided drug design arise from the difficulty of reliably
predicting the binding affinity of a small molecule to a biological target. There is thus a strong …

To speed up the drug-discovery process, molecular dynamics (MD) calculations performed
in GROMACS can be coupled to docking simulations for the post-screening analyses of …

Over the last decades, molecular simulations have spread through the drug discovery arena.
This trend is expected to continue in the foreseeable future thanks to increased performance …

Conspectus This Account highlights recent advances and discusses major challenges in
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …