# Docking of a nanobody and antigen without knowledge of the active sites of the proteins

**URL:** <https://ask.bioexcel.eu/t/docking-of-a-nanobody-and-antigen-without-knowledge-of-the-active-sites-of-the-proteins/4813>\
**Category:** HADDOCK\
**Created:** [February 7, 2024, 8:17pm UTC](https://ask.bioexcel.eu/t/docking-of-a-nanobody-and-antigen-without-knowledge-of-the-active-sites-of-the-proteins/4813 "2024-02-07T20:17:43Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![kfopuni](https://avatars.discourse-cdn.com/v4/letter/k/bbe5ce/32.png) [@kfopuni](https://ask.bioexcel.eu/u/kfopuni)\
**Post date:** [February 7, 2024, 8:17pm UTC](https://ask.bioexcel.eu/t/docking-of-a-nanobody-and-antigen-without-knowledge-of-the-active-sites-of-the-proteins/4813/1 "2024-02-07T20:17:43Z")

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How do I dock two proteins that I don’t know their active or passive sites? Thank you

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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:** [February 9, 2024, 3:36pm UTC](https://ask.bioexcel.eu/t/docking-of-a-nanobody-and-antigen-without-knowledge-of-the-active-sites-of-the-proteins/4813/2 "2024-02-09T15:36:01Z")

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You can use the ab-initio mode of HADDOCK (center of mass restraints or random AIRs), and will need to increase the sampling to e.g. 10000/400/400 for the number of models.

Or try some other docking software/server like cluspro for example