# Ab initio protein-protein docking

**URL:** <https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710>\
**Category:** HADDOCK\
**Created:** [December 2, 2020, 9:24am UTC](https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710 "2020-12-02T09:24:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Fusluns](https://avatars.discourse-cdn.com/v4/letter/f/9e8a1a/32.png) [@Fusluns](https://ask.bioexcel.eu/u/Fusluns)\
**Post date:** [December 2, 2020, 9:24am UTC](https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710/1 "2020-12-02T09:24:24Z")

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Dear Haddock team

I am unable to find interaction data for the two proteins I am trying to dock. While I am fully aware that Haddock was not created for ab initio docking, I read through the Haddock-Capri run and tried to use what was applicable for my task. Since I am using the web-based version I cannot continue unless i define active and passive residues, which I do not know for my proteins. Is there a possible workaround or a way to continue without defining interacting residues, even if the proteins are not similar or symmetrical?

Thank you in advance for your answer and your time

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [December 2, 2020, 9:55am UTC](https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710/2 "2020-12-02T09:55:16Z")

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You can do that using center of mass restraints, but you will need to request Guru access. If you are not sure how to request that, have a look at this other thread: [Guru and Expert privileges](https://ask.bioexcel.eu/t/guru-and-expert-privileges/2600)

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**Author:** ![ZJandova](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/zjandova/32/291_2.png) [@ZJandova](https://ask.bioexcel.eu/u/ZJandova)\
**Post date:** [December 2, 2020, 10:17am UTC](https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710/3 "2020-12-02T10:17:40Z")

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Hi,  
if you do not have any information about the interface you can also define all surface residues as passive (([https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/))) or define randomly ambiguous interaction restraints from accessible residues ([https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/)) . HADDOCK then offers you the possibility to change the relative solvent accessibility cutoff. More info about restraints definition in our best practice guide: [https://www.bonvinlab.org/software/bpg/restraints/](https://www.bonvinlab.org/software/bpg/restraints/)

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**Author:** ![Fusluns](https://avatars.discourse-cdn.com/v4/letter/f/9e8a1a/32.png) [@Fusluns](https://ask.bioexcel.eu/u/Fusluns)\
**Post date:** [December 2, 2020, 10:53am UTC](https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710/4 "2020-12-02T10:53:49Z")

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Thank you for the fast replies and your help.  
I guess I was confused by how to define random AIRs.  
I could proceed by defining the full length of both molecules as semi-flexible and then activating random patches in the docking parameter tab.

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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:** [December 2, 2020, 11:21am UTC](https://ask.bioexcel.eu/t/ab-initio-protein-protein-docking/2710/5 "2020-12-02T11:21:32Z")

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Let HADDOCK deals with the flexibly using the default automatic mode.