# Docking with small molecule

**URL:** https://ask.bioexcel.eu/t/docking-with-small-molecule/4430
**Category:** HADDOCK
**Created:** [July 27, 2023, 11:01am UTC](https://ask.bioexcel.eu/t/docking-with-small-molecule/4430 "2023-07-27T11:01:52Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![karenf](https://avatars.discourse-cdn.com/v4/letter/k/b5ac83/32.png) [@karenf](https://ask.bioexcel.eu/u/karenf)
#### Post date: [July 27, 2023, 11:01am UTC](https://ask.bioexcel.eu/t/docking-with-small-molecule/4430/1 "2023-07-27T11:01:52Z")

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I want to use HADDOCK to analyze the binding of a protein to receptor with and without a small molecule present.  
How do I know if the docking is altered by the presence of this molecule? What should I look for?

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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: [August 3, 2023, 10:21am UTC](https://ask.bioexcel.eu/t/docking-with-small-molecule/4430/2 "2023-08-03T10:21:24Z")

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If the ligand is close to the binding interface it might impact the energetics.

You can simply try the docking with and without the small ligand present and compare the results.