Other than the library size, are there any other major factors that influence the docking time?

It is not possible to determine how long a ligand or set of ligands will take to dock as this is dependent on, but not limited to, the following:

• the size of the defined binding site
• the size and flexibility of the ligand(s)
• the computer speed
• the GOLD configuration (e.g. docking runs that allow for flexible side chains or explicit water molecules will take longer)
• the number of GA runs per ligand
• whether or not "allow early termination" is switched on
• the chosen GA parameters​