# protein-dsDNA docking in HADDOCK 2.4

**URL:** <https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906>\
**Category:** HADDOCK\
**Created:** [April 11, 2020, 8:49pm UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906 "2020-04-11T20:49:12Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Q.E.D](https://avatars.discourse-cdn.com/v4/letter/q/51bf81/32.png) [@Q.E.D](https://ask.bioexcel.eu/u/Q.E.D)\
**Post date:** [April 11, 2020, 8:49pm UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906/1 "2020-04-11T20:49:13Z")

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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!

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [April 12, 2020, 7:19am UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906/2 "2020-04-12T07:19:51Z")

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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/](https://bianca.science.uu.nl/pdbtools/)

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

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<div class="post-metadata">

**Author:** ![Q.E.D](https://avatars.discourse-cdn.com/v4/letter/q/51bf81/32.png) [@Q.E.D](https://ask.bioexcel.eu/u/Q.E.D)\
**Post date:** [April 12, 2020, 4:24pm UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906/3 "2020-04-12T16:24:00Z")

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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?

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [April 12, 2020, 5:11pm UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906/4 "2020-04-12T17:11:08Z")

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Yes - correct

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

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<div class="post-metadata">

**Author:** ![Q.E.D](https://avatars.discourse-cdn.com/v4/letter/q/51bf81/32.png) [@Q.E.D](https://ask.bioexcel.eu/u/Q.E.D)\
**Post date:** [April 13, 2020, 6:34pm UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906/5 "2020-04-13T18:34:55Z")

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

Thanks!

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [April 14, 2020, 8:55am UTC](https://ask.bioexcel.eu/t/protein-dsdna-docking-in-haddock-2-4/1906/6 "2020-04-14T08:55:11Z")

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No it is not.

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