Active/passive residue selection with >2 molecules

HADDOCK
1

Hello,

I am a novel user, and although with some help of this platform I have made some progress in preparing my files for 2 molecule interactions, I am now faced with difficulties with using multiple molecules. My aim is to dock a putative epitope of a protein (PDB structure present, 2 chains (AB), coiled coils) onto my antibody. Via SAbPred, I have generated HC and LC PDB files of this antibody. Docking either HC or LC on one of the chains A or B of my protein works.
When I try to submit LC, HC and A, these come through without errors. However, I do not get through the input parameters.

I have tried the following:

  • leaving the active residues field blank for all, or for any of the three
  • indicating CDRs for the HC and LC, and putative 50 aa stretch containing epitope for A, and indicating for HC and LC that these interact with A and for A they interact with LC and HC
  • in addition to the above, as a second active/passive residues input field opens with multiple molecules, I indicated as above, and in the scond input field for HC and LC the entire sequence for possible interaction with each other. In addition, I separately indicated the epitope of A to interact with HC and LC in the two selection#x input fields.

Nevertheless, I fail to pass to submit. The tutorials are currently offline, I do not get error messages and the sidenotes don’t really help me.
I hope I can get some relevant info here.
Kind regards, and thank you for your effort,

Judy

2

Don’t dock separately the two chains of the antibody!

It should be treated as one molecule for docking purposes.

You will need to make sure that the two chains have no overlap in numbering.
Shifting the number can be done with our PDB-tools for which we have a brand new beta server:

wenmr.science.uu.nl/pdbtools

Our tutorials will hopefully soon reappear (Git Pages is doing some maintenance… outside our control)

3

Thank you,
as I got error messages when using mutliple strands in the PDB doc, so I tried with separate to see if it could work. But with some help I managed to adjust the file with pdbtools.

Waiting for my output now,

Best, Judy