# Request for Guidance on Analyzing Protein-Protein Docking Results

**URL:** <https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184>\
**Category:** HADDOCK\
**Created:** [July 9, 2024, 10:05am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184 "2024-07-09T10:05:19Z")\
**Posts on this page:** 1\
**Showing post:** 3

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**Author:** ![marco.giulini](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco.giulini/32/961_2.png) [@marco.giulini](https://ask.bioexcel.eu/u/marco.giulini)\
**Post date:** [July 9, 2024, 10:21am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/3 "2024-07-09T10:21:02Z")

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Hi,

The HADDOCK score should not be used to compare different complexes, but rather to inspect the results obtained within each run. Similar systems might be compared, but I don’t know how similar proteins B and C are in your case.

Have a look at this other thread [Problem with interpretation HADDOCK scores](https://ask.bioexcel.eu/t/problem-with-interpretation-haddock-scores/5038)

PS: I notice you have a very high restraint energy, maybe check your restraints and/or remove the 10% of that value from the overall HADDOCK score

Cheers

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