Dear Kristin,
Although this may give me some enemies to say this, I personally would not put docking into a patent. The number of incorrect docking poses I have seen is far greater than the number of incorrect crystal structures I have seen. If you do docking and confirm with a crystal structure, or start with a crystal structure and dock related compounds, you are on more solid ground. If you dock a novel scaffold into a novel target, then the docking is highly suspicious and anyone would be skeptical about it.
My personal view is a crystal structure does add value to a patent because it defines the binding mode of the compound. However, the reality is that many small molecule drug discovery patents don't include these data and authors instead will often publish the crystal structure in a journal after the patent comes out. You would have to consult your own IP group to see what their philosophy would be. Every attorney has their own personal views on this. In the world of biologics and antibodies, having a crystal structure is generally considered important because the IP is generally around the antibody-antigen interaction and having that epitope precisely defined and CDR sequences protected is important. (You don't want "rip-off biotech Inc" busting your IP by changing one residue in the CDR loop from V to I).
Good luck.
Nick
[This e-mail message may contain privileged, confidential and/or proprietary information of H3 Biomedicine. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.]