# Extrating Kd with HADDOCK3

**URL:** <https://ask.bioexcel.eu/t/extrating-kd-with-haddock3/6013>\
**Category:** HADDOCK\
**Tags:** haddock, support\
**Created:** [February 25, 2026, 8:15pm UTC](https://ask.bioexcel.eu/t/extrating-kd-with-haddock3/6013 "2026-02-25T20:15:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![BioMarc](https://avatars.discourse-cdn.com/v4/letter/b/58f4c7/32.png) [@BioMarc](https://ask.bioexcel.eu/u/BioMarc)\
**Post date:** [February 25, 2026, 8:15pm UTC](https://ask.bioexcel.eu/t/extrating-kd-with-haddock3/6013/1 "2026-02-25T20:15:54Z")

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Hello community,

We are using HADDOCK3 to identify potential binding sites of DNA aptamers on proteins. So far, we have been using the EMScoring score as the final parameter to distinguish our best candidates. We were wondering whether there is a way to extract a predicted Kd instead. If not, could you recommend any tools that could be used for this?

Thank you very much,  
Marc

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<div class="post-metadata">

**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 26, 2026, 3:00am UTC](https://ask.bioexcel.eu/t/extrating-kd-with-haddock3/6013/2 "2026-02-26T03:00:17Z")

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HADDOCK gives a score, which has arbitrary units because it is not a Kd.

I am not aware of a Kd prediction method for protein-DNA interactions (there must be some).  
We are working on an adaptation of our PRODIGY Kd predictor for nucleic acids though, but it will take some time.