# Refinement of Protein Structures with HADDOCK

**URL:** <https://ask.bioexcel.eu/t/refinement-of-protein-structures-with-haddock/4832>\
**Category:** Uncategorized\
**Created:** [February 14, 2024, 10:07am UTC](https://ask.bioexcel.eu/t/refinement-of-protein-structures-with-haddock/4832 "2024-02-14T10:07:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Curious](https://avatars.discourse-cdn.com/v4/letter/c/6bbea6/32.png) [@Curious](https://ask.bioexcel.eu/u/Curious)\
**Post date:** [February 14, 2024, 10:07am UTC](https://ask.bioexcel.eu/t/refinement-of-protein-structures-with-haddock/4832/1 "2024-02-14T10:07:18Z")

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Hello!

Using AlphaFold2 I built a model of a homodimeric protein that has a total of 3128 amino acid residues. 83.2% of its residues are in the most favored regions, 13.7% are in the additional allowed regions and 3.1% are in the generously allowed regions. I want to refine this model with HADDOCK2.4, but I have a few doubts. The first is which protocol to use. The choice depends on what? Should I use all the protocols? Is there a protocol that is the most widely used, for example “Water Refinement”? As for “Clustering”, should I leave “Method”, “Cutoff” and “Minimum cluster size” at FCC, 0.60 and 1 respectively? Or should I change it to RMSD, 2.0, 1? In “Analysis parameters”, should I leave “Cluster” or change it to “Full”? I looked for this information in the tutorials provided, but couldn’t find it. I haven’t found how to interpret the results either.

Another question I have does not concern HADDOCK2.4, but the refinement itself. According to your experience, should refinement be carried out until 98% residue is reached in the most favorable regions of the Ramachandran graph, or is refining just once enough since refining doesn’t always improve anything?

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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 14, 2024, 10:34am UTC](https://ask.bioexcel.eu/t/refinement-of-protein-structures-with-haddock/4832/2 "2024-02-14T10:34:57Z")

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In this case I would use the standard water refinement protocol. Assuming you don’t have too many clashes.

About the most favourable Ramachandra percentages, you should not expect to reach 98% … This is not what you observe in experimental structures… And longer refinement protocols will not per se improve those percentages

More reading about refinement protocols and their performance:

- T Neijenhuis, S.C. van Keulen and **A.M.J.J. Bonvin**. [Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4](https://doi.org/10.1016/j.str.2022.02.001). _Structure_ _30_, 476-484 (2022).

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**Author:** ![Curious](https://avatars.discourse-cdn.com/v4/letter/c/6bbea6/32.png) [@Curious](https://ask.bioexcel.eu/u/Curious)\
**Post date:** [February 14, 2024, 11:46am UTC](https://ask.bioexcel.eu/t/refinement-of-protein-structures-with-haddock/4832/3 "2024-02-14T11:46:49Z")

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Copy that! You helped me a lot, thank you very much!