Docking of two domains linked by unstructured region

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

Dear Developers!

Can I set up a run on the webserver or locally, if the interacting domains are in the same polypeptide chain?
I would like to model the binding orientation to each other, and also the unstructured linker region between them. I can define several restraints for the interaction from mutation and NMR studies, and also have SAXS data of the linked domains.

Is there any possibility to do that?

Thank you for your kind reply!

2

Simply treat them as separate domains, cutting the link region and defining it as fully flexible.
And add a distance restraint to connect them.
Also make sure to define the C- and N-termini of the two domains as uncharged.

You will only be able to use SAXS data for scoring.

An alternative might be to look at the ATSAS software suite which will model against the SAXS data - but without flexibility at the interface