protein-dsDNA docking in HADDOCK 2.4

HADDOCK
1

Hi

HADDOCK 2.4 is a great tool for my research. I’d like to perform a protein and double-stranded DNA docking using HADDOCK 2.4. However, it seems I can only select one chain of the DNA structure when running the server. Is it possible to do the docking using both strands of the DNA and the protein?

Thanks!

2

You should shift the numbering of the second strand so that it does not overlap and give the resulting PDB as one molecule to HADDOCK.

This can be done for example with our PDB tools for which we are a brand new server:

https://bianca.science.uu.nl/pdbtools/

Select the second chain and use pdb_shiftres to shift the residue numbering

3

Thanks!

So if I have a dsDNA in a PDB where chain A has residues labeled from 1-20, and chain B has residues labeled from 1-10. I should use pdb_shiftres to re-label the second chain to have IDs 21-31?

Do I need to change the ID of the second chain from B to A?

4

Yes - correct

And no need to change the chain labels as long as you tell haddock to use all chains

5

Is this equivalent to using three molecules in haddock input – protein chain, DNA chain A, and DNA chain B?

Thanks!

6

No it is not.

You do not want to dock the two strands of your DNA separately…

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