Possibility of adding residue restraints

[wjs20]

I tried running GeoDock with a VH-VL antibody complex + its protein antigen. GeoDock succesfully generated a docked structure, but it looks like the antigen is bound on the opposite side of the VH-VL to the CDRs (i.e. in what would be the buried V-domain - C-domain interface were the C-domain included in the structure file). I have attached a picture.

Would there be any way to specify regions to exlude from the docking computation? e.g. say confine it to the CDRs of the antibody only?

[julianrfaust]

What you are describing is essentially DockGPT by McPartlon and Xu which is the best fast Ab-Ag docking model in literature and can also take in contacts though the code isn’t fully released - likely due to a commercial venture MoleculeMind mentioned in the paper. Implementing this model can be done with some effort. The GeoDock code has a SabDab loader too which may have been attempted but was not mentioned in the GeoDock paper. Fine tuning the GeoDock model on SabDab seems promising.