I have a two-domain protein and I’m wondering if it’s possible to use Haddock to model the contacts and relative orientation between those two domains using chemical shift perturbations. Thanks!
Yes of course! Simply treat your two domains as separate molecules, possibly defining their junctions as fully flexible and adding distance restraints to keep them in proximity.
Thank you so much!
Do I first define the junction by HingeProt, and make two PDB files of the separated domains as inputs for HADDOCK, and then just have some distance restraints in the AIR file? If I do it this way, the resulting models would be two separate domains contacting each other, correct? Is there an example or reference somewhere that describes how to do these in more detail? Sorry. I’m pretty new to HADDOCK.
We used a similar approach for dealing with large conformational changes.
Check:
• E. Karaca and A.M.J.J. Bonvin A multi-domain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure, 19 555-565(2011).