Docking with no experimental data

HADDOCK
1

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:

Regards
Dan.

2

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”

3

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.

Cheers,
Dan.