# Comparison of Haddock Scores between different Complexes

**URL:** <https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059>\
**Category:** HADDOCK\
**Created:** [December 28, 2022, 1:50pm UTC](https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059 "2022-12-28T13:50:16Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![marianvincenzi](https://avatars.discourse-cdn.com/v4/letter/m/a88e4f/32.png) [@marianvincenzi](https://ask.bioexcel.eu/u/marianvincenzi)\
**Post date:** [December 28, 2022, 1:50pm UTC](https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059/1 "2022-12-28T13:50:16Z")

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Is it correct to compare the Haddock scores of docking analyses from different complexes (same protein with different peptide ligands with equal number of residues and a few mutations of a common motif) to determine which “complex is better” and which “complex is worse”?

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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:** [December 28, 2022, 7:03pm UTC](https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059/2 "2022-12-28T19:03:54Z")

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This is indeed ok, but this is not a ddG (change in binding affinity)

Also it all depends on how you setup you docking (e.g. do you have good information to guide the docking).

An alternative would be, giving a good model or structure of one protein-peptide complex, only use the refinement interface and compare the various mutants.

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**Author:** ![Andrea\_Spitaleri](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/andrea_spitaleri/32/37_2.png) [@Andrea\_Spitaleri](https://ask.bioexcel.eu/u/Andrea_Spitaleri)\
**Post date:** [December 29, 2022, 7:26am UTC](https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059/3 "2022-12-29T07:26:39Z")

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In addition to that you may run MM/PBSA approach - see [dMMPBSA](https://www.frontiersin.org/articles/10.3389/fmolb.2016.00046/full)

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**Author:** ![marianvincenzi](https://avatars.discourse-cdn.com/v4/letter/m/a88e4f/32.png) [@marianvincenzi](https://ask.bioexcel.eu/u/marianvincenzi)\
**Post date:** [January 3, 2023, 2:23pm UTC](https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059/4 "2023-01-03T14:23:38Z")

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Thank you very mucj for answering.

This answer leads to another question sorry…

The refinement interface should be used after having generated a model of the complex (e.g. by docking run) in order to optimize a structure already available ? or the the best complex structure generated by refinement interface can be used directly for the comaparison ?

Thank you again

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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:** [January 3, 2023, 4:05pm UTC](https://ask.bioexcel.eu/t/comparison-of-haddock-scores-between-different-complexes/4059/5 "2023-01-03T16:05:16Z")

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If you have a model or structure of the wild type complex, you could simply make mutations in it and then use the refinement interface. I.e. no docking