Without controls, it is difficult to ascertain how well docking is performing, short of running a prospective screen. While ligand-free evaluation is not yet supported, its future incorporation into DockOpt is planned. Until then, we recommend using Blastermaster in the absence of known ligands. Blastermaster uses sensible, typical values for the parameters otherwise optimized by DockOpt. For instructions on how to install Pydock3 and use Blastermaster, see Supporting Information S1.