Docking with no experimental data

Dear Haddock users,

I am trying to dock a metalloprotein with a post-translational modification (PTM) to a sequence of DNA, however no experimental evidence exists for the protein-DNA complex as for the atomic/residue interactions that take place.

I essentially want to dock the metalloprotein with PTM and DNA together to perform MD simulations on them, how can I dock these together without defining active/passive residues as I dont know which are active/passive.

Thank you in advance! :slight_smile:


Have a look at the Best Practices Guide and the ab initio docking tutorial and also the peptide section

Aditionally, if you are combining docking and MD, these might be useful to you:

Jandova, Z., Vargiu, A. V. & Bonvin, A. M. J. J. Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue. Journal of Chemical Theory and Computation vol. 17 5944–5954 (2021).

short talk was delivered by Zuzana Jandova: “When HADDOCK meets GROMACS

Hello @honoratorv

Thank you for your response.

I will take a look at the tutorials and papers recommended and get back to you if I get into trouble.


Hello @honoratorv ,

I am sorry for the very late reply, but I am trying to implement the solutions provided in the ab-initio tutorial. I am slightly confused by the Noncrystallographic symmetry restraints (NCS). I have the metalloprotein I wish to dock to DNA, so for the NCS segment pairs do I have one pair (A-B)?

Secondly if I have only a single pair, what do I use for segment 1 and 2, do I use the residue numbers 1-41 (A) and segment (B) 1-30 for example?


Do you have any symmetry in your system?

NCS should be applied to exactly the same molecules.


See more information about NCS restraints here,

but in summary:

The NCS option imposes non-crystallographic symmetry restraints: It enforces that two molecules, a fraction thereof or even two sub-domains within the same molecule should be identical without defining any symmetry operation between them

but based in your first response:

You seem to not have any information if its a symmetric complex, in that case you can look into the Best Practices Guide in the section: Information about the interface is not available. For your case it seems that you can try random interactions, surface contacts or center of mass restraints. The links and relevant information are all in the guide, and these options are also accessible via the web interface!

Hello @amjjbonvin @honoratorv

I don’t believe I have symmetry within the system, but I will try the guide suggested.

Thanks again! :slight_smile:

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Then symmetry and NCS restraints are irrelevant