# Compare HADDOCK scores

**URL:** <https://ask.bioexcel.eu/t/compare-haddock-scores/2878>\
**Category:** HADDOCK\
**Created:** [March 30, 2021, 5:29am UTC](https://ask.bioexcel.eu/t/compare-haddock-scores/2878 "2021-03-30T05:29:11Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Abhi](https://avatars.discourse-cdn.com/v4/letter/a/b487fb/32.png) [@Abhi](https://ask.bioexcel.eu/u/Abhi)\
**Post date:** [March 30, 2021, 5:29am UTC](https://ask.bioexcel.eu/t/compare-haddock-scores/2878/1 "2021-03-30T05:29:11Z")

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I am docking 1 protein with 5-6 ssDNA sequences. How do I find out which is the best ligand? as you don’t give binding energy for DNA-protein docking.  
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:** [March 30, 2021, 6:37am UTC](https://ask.bioexcel.eu/t/compare-haddock-scores/2878/2 "2021-03-30T06:37:45Z")

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We don’t have a solution for this I am afraid…

If the protein is the same (i.e. a constant), scores might be better indicative of preferences for binding.  
But this has never been tested for protein-ssDNA.

The only advice would be to find systems for which you know the answer and test if you can fish out the correct sequence.  
Not easy in our hands…