Homologous protein complex modeling

HADDOCK
1

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.

– Maurizio

2

Dear Maurizio

Yes it’s possible. Two ways:

  1. model your individual proteins, superimpose them on the reference complex and refine the model via the refinement interface of HADDOCK

  2. derive CA-CA distance restraints from the reference complex and use those for docking.
    This is described in the following tutorial:

    http://www.bonvinlab.org/education/HADDOCK/HADDOCK-CACA-guided/

Relevant reference:

• 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).

  https://academic.oup.com/bib/article/18/3/458/2562753

Cheers
Alexandre