# Protein Refinement

**URL:** <https://ask.bioexcel.eu/t/protein-refinement/4899>\
**Category:** HADDOCK\
**Created:** [April 3, 2024, 1:39pm UTC](https://ask.bioexcel.eu/t/protein-refinement/4899 "2024-04-03T13:39:28Z")\
**Posts on this page:** 4\
**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:** [April 3, 2024, 1:39pm UTC](https://ask.bioexcel.eu/t/protein-refinement/4899/1 "2024-04-03T13:39:28Z")

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Hello, what web server protein refinement tool can you recommend? I tried to use Galaxy Refine, but HADDOCK does not accept refined PDB. “ATOM/HETATM line does not meet the expected format” this is what pops up every time I use the refined PDB in HADDOCK.

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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:** [April 3, 2024, 2:06pm UTC](https://ask.bioexcel.eu/t/protein-refinement/4899/2 "2024-04-03T14:06:45Z")

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Hi! you may want to check out the [HADDOCK refinement interface](https://bianca.science.uu.nl/haddock2.4/refinement/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:** [April 4, 2024, 2:19am UTC](https://ask.bioexcel.eu/t/protein-refinement/4899/3 "2024-04-04T02:19:20Z")

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Hello, HADDOCK refinement interface removes my protein bad angles and bonds. However, it does not improve my Ramachandran analysis result.

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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:** [April 4, 2024, 5:59pm UTC](https://ask.bioexcel.eu/t/protein-refinement/4899/4 "2024-04-04T17:59:54Z")

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It is only a very short refinement… No miracles.

Check our article about refining complexes to get an idea of what can be done / achieved.

- 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).