Users are presented with multiple strategies for binding site selection. The Reference and RoG (radius of gyration) options make use of a co-crystallized ligand, which needs to be supplied as a separate file. Alternatively, an already docked pose could also be used. In the Reference method, DockM8 automatically determines the ligand's center of mass (CoM) and defines a box (the dimensions of which can be specified by the user) around this CoM. The RoG method determines the box's center coordinates in the same way as before but uses the previously defined reference ligand's radius of gyration (RoG) to define the box size. This was shown to be a suitable method to determine box size for AutoDock Vina . Alternatively, if no crystal ligand is available, DockM8 can make use of the DoGSiteScorer algorithm which combines pocket finding along with pocket characterization to select druggable binding sites . DockM8's query of DoGSiteScorer via the proteins.plus webserver outputs the largest binding site by default. An option to select binding sites based on other metrics provided by DogSiteScorer is also included (available metrics are: Volume, Surface, Depth and Druggability Score). Finally, the user can supply custom box center and size values, both in the GUI and by command line. Details can be found in the DockM8 Usage Guide. The binding site definition is then used for all further docking and rescoring functions.