# Determining domain-domain contacts by HADDOCK
**URL:** https://ask.bioexcel.eu/t/determining-domain-domain-contacts-by-haddock/207
**Category:** HADDOCK
**Created:** [September 20, 2016, 10:24pm UTC](https://ask.bioexcel.eu/t/determining-domain-domain-contacts-by-haddock/207 "2016-09-20T22:24:06Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@yizhis](https://ask.bioexcel.eu/u/yizhis)
#### Post date: [September 20, 2016, 10:24pm UTC](https://ask.bioexcel.eu/t/determining-domain-domain-contacts-by-haddock/207/1 "2016-09-20T22:24:06Z")
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!
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 21, 2016, 6:12am UTC](https://ask.bioexcel.eu/t/determining-domain-domain-contacts-by-haddock/207/2 "2016-09-21T06:12:30Z")
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.
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### Author:  [@yizhis](https://ask.bioexcel.eu/u/yizhis)
#### Post date: [September 21, 2016, 2:21pm UTC](https://ask.bioexcel.eu/t/determining-domain-domain-contacts-by-haddock/207/3 "2016-09-21T14:21:22Z")
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.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 21, 2016, 2:51pm UTC](https://ask.bioexcel.eu/t/determining-domain-domain-contacts-by-haddock/207/4 "2016-09-21T14:51:36Z")
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).
```
[http://dx.doi.org/doi:10.1016/j.str.2011.01.014](http://dx.doi.org/doi:10.1016/j.str.2011.01.014)