# HADDOCK Refinement

**URL:** <https://ask.bioexcel.eu/t/haddock-refinement/4785>\
**Category:** HADDOCK\
**Created:** [February 2, 2024, 2:34pm UTC](https://ask.bioexcel.eu/t/haddock-refinement/4785 "2024-02-02T14:34:56Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Aron\_1226](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aron_1226/32/918_2.png) [@Aron\_1226](https://ask.bioexcel.eu/u/Aron_1226)\
**Post date:** [February 2, 2024, 2:34pm UTC](https://ask.bioexcel.eu/t/haddock-refinement/4785/1 "2024-02-02T14:34:56Z")

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Hello! Questions:

1.) Can I use the HADDOCK 2.4 Refinement, to refine my PDB/protein models that will be used for protein-protein docking?  
2.) Should I refine my docked protein-protein complex?

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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:** [February 2, 2024, 2:48pm UTC](https://ask.bioexcel.eu/t/haddock-refinement/4785/2 "2024-02-02T14:48:42Z")

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> 1.) Can I use the HADDOCK 2.4 Refinement, to refine my PDB/protein models that will be used for protein-protein docking?

Yes - the refinement server will also accept single molecules (and not only complexes)

> 2.) Should I refine my docked protein-protein complex?

You could (e.g. if you want to remove the contribution of the restraints ) but not really needed in principle

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**Author:** ![Aron\_1226](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aron_1226/32/918_2.png) [@Aron\_1226](https://ask.bioexcel.eu/u/Aron_1226)\
**Post date:** [February 2, 2024, 4:03pm UTC](https://ask.bioexcel.eu/t/haddock-refinement/4785/3 "2024-02-02T16:03:46Z")

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Hello, Professor!

1. What is the benefit if I refine my PDB/protein model prior to my docking? Does it improve the structure of my model?

2. If I refine my docked protein-protein complex, does it also improve the binding of my complex?

3. Is it ok if I only use the water refinement and energy minimization refinement? Or should I use all the available refinement methods?

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**Author:** ![Aron\_1226](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aron_1226/32/918_2.png) [@Aron\_1226](https://ask.bioexcel.eu/u/Aron_1226)\
**Post date:** [February 5, 2024, 8:32am UTC](https://ask.bioexcel.eu/t/haddock-refinement/4785/4 "2024-02-05T08:32:44Z")

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Hello, Professor @amjjbonvin , I would like to follow up on my last question. Thank you!

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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:** [February 5, 2024, 8:45am UTC](https://ask.bioexcel.eu/t/haddock-refinement/4785/5 "2024-02-05T08:45:08Z")

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> What is the benefit if I refine my PDB/protein model prior to my docking? Does it improve the structure of my model?

It all depends on how good or bad your model was… It would remove clashes if present.

> 1. If I refine my docked protein-protein complex, does it also improve the binding of my complex?

It might… or not…

> 1. Is it ok if I only use rhe water refinement and energy minimization refinement? Or should I use all the available refinement method?

Water refinement only