# Protein-peptide scoring function

**URL:** <https://ask.bioexcel.eu/t/protein-peptide-scoring-function/2919>\
**Category:** HADDOCK\
**Created:** [May 12, 2021, 8:52am UTC](https://ask.bioexcel.eu/t/protein-peptide-scoring-function/2919 "2021-05-12T08:52:55Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sandra.romero](https://avatars.discourse-cdn.com/v4/letter/s/2acd7d/32.png) [@sandra.romero](https://ask.bioexcel.eu/u/sandra.romero)\
**Post date:** [May 12, 2021, 8:52am UTC](https://ask.bioexcel.eu/t/protein-peptide-scoring-function/2919/1 "2021-05-12T08:52:55Z")

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Dear Haddock team,

I would like to employ the Haddock scoring function to predict the binding affinity of a set of protein-peptide complexes. How could I do that with out the docking step?

Thanks!  
Sandra

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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:** [May 12, 2021, 9:43am UTC](https://ask.bioexcel.eu/t/protein-peptide-scoring-function/2919/2 "2021-05-12T09:43:19Z")

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You can use the refinement interface - but no warranty the HADDOCK score has any correlation with binding affinity… 🙂

```
https://wenmr.science.uu.nl/haddock2.4/refinement/1
```

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<div class="post-metadata">

**Author:** ![sandra.romero](https://avatars.discourse-cdn.com/v4/letter/s/2acd7d/32.png) [@sandra.romero](https://ask.bioexcel.eu/u/sandra.romero)\
**Post date:** [May 13, 2021, 12:21pm UTC](https://ask.bioexcel.eu/t/protein-peptide-scoring-function/2919/3 "2021-05-13T12:21:00Z")

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Thank you very much for the information.

I was looking for the function dMM-PBSA ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006095/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006095/)) in the webserver. It is here implemented? Or could be Prodigy the most appropriate it method for BA prediction?

Thanks!  
Sandra

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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:** [May 14, 2021, 11:52am UTC](https://ask.bioexcel.eu/t/protein-peptide-scoring-function/2919/4 "2021-05-14T11:52:06Z")

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Hi Sandra,

the dMM-PBSA is not implemented in the server.  
Best to contact Andrea Spitaleri for the scripts.