# Kd patent in prodigy

**URL:** <https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200>\
**Category:** PRODIGY\
**Created:** [March 19, 2023, 10:16pm UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200 "2023-03-19T22:16:46Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Nil](https://avatars.discourse-cdn.com/v4/letter/n/a183cd/32.png) [@Nil](https://ask.bioexcel.eu/u/Nil)\
**Post date:** [March 19, 2023, 10:16pm UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200/1 "2023-03-19T22:16:46Z")

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Hi Everyone, after I uses prodigy analysis for protein-protein doc , Kd option is 3.9e-08, and 4.5e-08!  
Can you help me to know what exactly Kd measure in these process? And which of them is better ?

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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 20, 2023, 12:20am UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200/2 "2023-03-20T00:20:34Z")

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Read the original PRODIGY paper 🙂

And what do you mean exactly by PRODIGY gives me two options?  
There is only one value returned per prediction.

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**Author:** ![Nil](https://avatars.discourse-cdn.com/v4/letter/n/a183cd/32.png) [@Nil](https://ask.bioexcel.eu/u/Nil)\
**Post date:** [March 20, 2023, 7:47am UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200/3 "2023-03-20T07:47:40Z")

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Hi professor, these options for 2 samples (WT and mutant) , I mentioned for which one is better about binding affinity

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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 20, 2023, 8:36am UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200/4 "2023-03-20T08:36:27Z")

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The smaller the predicted Kd the higher the binding affinity.

But PRODIGY has not been parametrised on ddG values… so use with care 🙂

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<div class="post-metadata">

**Author:** ![Nil](https://avatars.discourse-cdn.com/v4/letter/n/a183cd/32.png) [@Nil](https://ask.bioexcel.eu/u/Nil)\
**Post date:** [March 20, 2023, 9:59am UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200/5 "2023-03-20T09:59:48Z")

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I really want to thank you for your help dear professor