# Docking with protein embedded in a bacterial membrane

**URL:** <https://ask.bioexcel.eu/t/docking-with-protein-embedded-in-a-bacterial-membrane/5925>\
**Category:** Uncategorized\
**Created:** [October 31, 2025, 3:36am UTC](https://ask.bioexcel.eu/t/docking-with-protein-embedded-in-a-bacterial-membrane/5925 "2025-10-31T03:36:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\
**Post date:** [October 31, 2025, 3:36am UTC](https://ask.bioexcel.eu/t/docking-with-protein-embedded-in-a-bacterial-membrane/5925/1 "2025-10-31T03:36:53Z")

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Good day! I would like to ask if I can dock my protein embedded in a bacterial membrane using haddock2.4? I built the system using charmm gui membrane builder. 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:** [October 31, 2025, 7:33am UTC](https://ask.bioexcel.eu/t/docking-with-protein-embedded-in-a-bacterial-membrane/5925/2 "2025-10-31T07:33:30Z")

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I have seen membrane embedded systems and also nanodisks.  
If you bacterial membrane is complex with LPS and all kind of other things, it might not work though. You will have to try.

But do you need the explicit membrane for what you want to do?