# Protein preparation for docking

**URL:** <https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137>\
**Category:** HADDOCK\
**Created:** [February 24, 2023, 2:59pm UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137 "2023-02-24T14:59:13Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![nidhi](https://avatars.discourse-cdn.com/v4/letter/n/a5b964/32.png) [@nidhi](https://ask.bioexcel.eu/u/nidhi)\
**Post date:** [February 24, 2023, 2:59pm UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137/1 "2023-02-24T14:59:13Z")

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is protein preparation required before submission to HADDOCK2.4 server?

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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 24, 2023, 6:51pm UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137/2 "2023-02-24T18:51:25Z")

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What do you mean by that exactly?

It also all depends where you protein is coming from?

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**Author:** ![nidhi](https://avatars.discourse-cdn.com/v4/letter/n/a5b964/32.png) [@nidhi](https://ask.bioexcel.eu/u/nidhi)\
**Post date:** [February 25, 2023, 4:51am UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137/3 "2023-02-25T04:51:09Z")

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if it is homology model? do we need to prepare it by adding charges/hydrogen before submission to HADDOCK?  
and if the protein structure is downloaded from PDB ?

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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 27, 2023, 12:53pm UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137/4 "2023-02-27T12:53:40Z")

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No need to add missing atoms. HADDOCK will deal with that.

When using PDB files, make sure to remove any junk (e.g. small molecules from the crystallisation buffer, water, unneeded chains…). Never use blindly a PDF file. Look at its content!

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [February 27, 2023, 2:26pm UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137/5 "2023-02-27T14:26:37Z")

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Structure preparation is covered in our Best Practices Guide, please have a look at it and let us know if there are still any questions;

> **[– Bonvin Lab](https://www.bonvinlab.org/software/bpg/)**

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<div class="post-metadata">

**Author:** ![nidhi](https://avatars.discourse-cdn.com/v4/letter/n/a5b964/32.png) [@nidhi](https://ask.bioexcel.eu/u/nidhi)\
**Post date:** [March 6, 2023, 5:52am UTC](https://ask.bioexcel.eu/t/protein-preparation-for-docking/4137/6 "2023-03-06T05:52:32Z")

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thank you for the clarification.