# HADDOCK score interpretation of different complexes

**URL:** <https://ask.bioexcel.eu/t/haddock-score-interpretation-of-different-complexes/4336>\
**Category:** HADDOCK\
**Created:** [May 22, 2023, 4:01pm UTC](https://ask.bioexcel.eu/t/haddock-score-interpretation-of-different-complexes/4336 "2023-05-22T16:01:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![deovine](https://avatars.discourse-cdn.com/v4/letter/d/bbce88/32.png) [@deovine](https://ask.bioexcel.eu/u/deovine)\
**Post date:** [May 22, 2023, 4:01pm UTC](https://ask.bioexcel.eu/t/haddock-score-interpretation-of-different-complexes/4336/1 "2023-05-22T16:01:49Z")

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Hello, I just need some clarifications regarding the do and don’ts of analyzing HADDOCK score here  
[https://www.bonvinlab.org/software/bpg/analysis/](https://www.bonvinlab.org/software/bpg/analysis/)

It is said that

> **Dont:** take scores as proxies of binding affinity to compare different complexes

> **Do Instead:** compare scores only within the same system/complex (i.e. to distinguish models for one docking run), or in the case of mutations

Does it mean that we cannot compare the HADDOCK scores of same peptide docked with two different proteins? But we can compare the HADDOCK score of a protein docked with a peptide and the same protein docked with the mutated version of the same peptide?

Thank you in advance.

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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 22, 2023, 6:19pm UTC](https://ask.bioexcel.eu/t/haddock-score-interpretation-of-different-complexes/4336/2 "2023-05-22T18:19:55Z")

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That’s pretty much it.

The more of the system remains constant the more reliably you can compare scores.

But the disclaimer remains: score is not equal to binding affinity… 🙂