DNA-Protein Docking

HADDOCK
1

Hello ,

I am using Haddock on my local machine.

  1. Is it possible to dock a DNA PDB to a protein with 2 chains? I am trying to do so after i used pdb_tidy from pdb tools but i am getting a RuntimeError(reason). Should i combine the 2 chains and if so how can i do it ?
  2. Is it possible to do the docking without the tbl file since I dont know which residues are involved in the docking ?

Thank you in advance!

2
  1. Is it possible to dock a DNA PDB to a protein with 2 chains? I am trying to do so after i used pdb_tidy from pdb tools but i am getting a RuntimeError(reason). Should i combine the 2 chains and if so how can i do it ?

The forum is searchable :slight_smile:

E.g. https://ask.bioexcel.eu/t/dealing-with-dimers/42

In short you will have to make your dimer a single chain with non-overlapping residue numbering.

Also described for example in:

[

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Low-sampling antibody-antigen modelling tutorial using a local version of HADDOCK3
bonvinlab.org

](Low-sampling antibody-antigen modelling tutorial using a local version of HADDOCK3 – Bonvin Lab)

and

[

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How to prepare structures for HADDOCK?
bonvinlab.org

](How to prepare structures for HADDOCK? – Bonvin Lab)

3

Thank you so much Dr. Bonvin !

Searched a bit further and i managed to make it work.
Enjoyed learning about the software !

Bonne soirée !