Ambiguity with protein dimer docking using crosslinking restraints

Dear HADDOCK users,

I’m modeling a protein dimer by docking two subunits. I have crosslinking data (5 crosslinks: 3 with EDC and 2 with BS3 crosslinker). When I started to summarize my restraints into a file I was faced with a dilemma: how to account for the amibiguity of those restrains since I don’t know whether there is a A356-B234 or A234-B356 crosslink and so on with the other crosslinks (where A and B correspond to chain IDs of the subunits). I’m using the restraints to specify the maximum distance between the crosslinked residues.

Many thanks in advance for any hints on how to specify the restraints properly!


Hello Miha,

You can define the two ambiguous possibilities for each cross-link and use HADDOCK default behavior that randomly excludes a fraction of ambiguous restraints (by default 50%) during a run.

So I’d just advise to add all combination matching your crosslinking experiments.

If you want to see if your distance retraints are consistent between each other and then refine your list, you can also use DisVis (

I hope this will help,


I also suggest you to take a look at two of our online tutorials that should be of interest for your kind of work:

DisVis web server tutorial: A small introduction into DisVis to analyse the interaction space between two molecules from a set of restraints. It can help to filter out putative false positive restraints and predict key residues involved in the interaction from this set of restraints. It makes use of our web portal (does not require Linux).

HADDOCK MS cross-links tutorial: A tutorial demonstrating the use of cross-linking data from mass spectrometry to guide the docking in HADDOCK. This tutorial builds on our DisVis tutorial and illustrates various scenarios of using cross-linking data in HADDOCK. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.

Ohhh, thanks to you both for suggestions! I didn’t notice the MS crosslinks tutorial and was a little bit lost :slight_smile:
Thanks again!