Getting Started
Getting Started with Docking
There are exceptions to every rule. Please do not use this guide as a substitute for common sense.
Docking requires a structure of the target to dock to.
Target structure available
If you have only one structure available, then that is probably the one you should use. If you have more than one structure, then you will probably need to pick a single structure to dock to. You may also be able to use multiple structures in various ways to inform your docking.
Generally, ligand-bound crystal structures are preferable to apo-enzyme crystal structures, which in turn are preferable to NMR structures, which in turn are preferable to homology or hand-built models. High resolution, problem free structures are better than lower resolution structures, or structures with problems.
You may still be able to dock to a homology model of your target, if you know the sequence. Try using ModBase.
Before docking, you should take a close look at the features of your crystal structure.