DockM8 gives users the option to prepare protein structures through querying the Protoss program via the proteins.plus webserver . Protoss optimizes the hydrogen bonding network in protein-ligand complexes, addressing the complexities of hydrogen bonding, tautomerism, and ionization to enable precise analysis of binding modes and calculation of associated binding energies . This provides streamlined access to ready-to-dock protein structures. Currently, DockM8 does not allow for modification of these automatically assigned protonation states, which may be critical in certain targets. In these cases, we encourage users to carefully modify the protein input file beforehand using the tools of their choice (e.g. PyMOL ).