Features of your target structure

Depending on the structural features of the target model, you may need to take special steps to prepare for docking. Many of the following points are relevant no matter which docking program you may use. Comments that are specific to a particular version or particular kind of docking program are noted.

Covalent inhibitor bound

If the target model you wish to dock to has a covalent inhibitor bound, your first step is obviously to remove the inhibitor. You should also keep in mind, however, that the covalently bound ligand may have distorted the active site in ways that a non-covalently bound ligand would not. If you have access to a structure with a non-covalently bound ligand, examine the differences - it may well be preferable to use the non-covalently bound ligand form of the target.