# Same protein and ligand but different active residues

**URL:** <https://ask.bioexcel.eu/t/same-protein-and-ligand-but-different-active-residues/5094>\
**Category:** HADDOCK\
**Created:** [June 4, 2024, 12:31am UTC](https://ask.bioexcel.eu/t/same-protein-and-ligand-but-different-active-residues/5094 "2024-06-04T00:31:39Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![may](https://avatars.discourse-cdn.com/v4/letter/m/58f4c7/32.png) [@may](https://ask.bioexcel.eu/u/may)\
**Post date:** [June 4, 2024, 12:31am UTC](https://ask.bioexcel.eu/t/same-protein-and-ligand-but-different-active-residues/5094/1 "2024-06-04T00:31:39Z")

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Hello

Im performing a docking analysis with a protein and a small ligand and doing two different runnings with the same files and parameters, but Im selecting differents active residues.

Can I compare these two results? Is it correct to assume if the smallest score may indicate the better binding site for the ligand?

Thanks!

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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:** [June 4, 2024, 5:19am UTC](https://ask.bioexcel.eu/t/same-protein-and-ligand-but-different-active-residues/5094/2 "2024-06-04T05:19:29Z")

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Best would be to compare the score of the two runs after removing the restraint energy from the score (subtract 10% of the restraint energy from the HADDOCK score).