Hi, I need to model a human protein complex. The structure of the same complex from a not mammalian organism is available.
I wonder if it is possible to use the entire complex as a template for homology modeling with HADDOCK. I would prefer such an approach instead of the usual docking between single modeled subunits.
Thanks for the help.
Yes it’s possible. Two ways:
model your individual proteins, superimpose them on the reference complex and refine the model via the refinement interface of HADDOCK
derive CA-CA distance restraints from the reference complex and use those for docking.
This is described in the following tutorial:
• Li C Xue, João P G L M Rodrigues, Drena Dobbs, Vasant Honavar, Alexandre M J J Bonvin.
Template-based protein–protein docking exploiting pairwise interfacial residue restraints.
Briefings in bioinformatics 18, 458-466 (2017).