# Protein and peptide ligand docking

**URL:** <https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877>\
**Category:** HADDOCK\
**Created:** [September 3, 2025, 2:45am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877 "2025-09-03T02:45:38Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Eugeneng991031](https://avatars.discourse-cdn.com/v4/letter/e/8dc957/32.png) [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\
**Post date:** [September 3, 2025, 2:45am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877/1 "2025-09-03T02:45:38Z")

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Hi, sorry for once again for bothering , I am now interested in docking the HLA-E nonamer peptide , VMAPRTLFL, with the receptor proteins of NKG2A/CD94. Is it wise to have the docking parameters setup as mentioned in [https://www.bonvinlab.org/education/HADDOCK-binding-sites/](https://haddock%20tutorial)#ab-initio-surface-based-docking-with-haddock ?

Also , shall I Fix molecule at its original position during it0 for the receptor protein?

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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:** [September 3, 2025, 11:29am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877/2 "2025-09-03T11:29:19Z")

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And you have no knowledge of the binding site on the receptor side?  
This seems a MHC-like receptor and usually the binding of peptide occurs through well defined anchor residues (positions 2 and 7 in the peptide).

The ligand binding site tutorial does not make sense in this case

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<div class="post-metadata">

**Author:** ![Eugeneng991031](https://avatars.discourse-cdn.com/v4/letter/e/8dc957/32.png) [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\
**Post date:** [September 3, 2025, 12:04pm UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877/3 "2025-09-03T12:04:06Z")

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For my knowledge , yes the peptide on position 2and 7 are anchor to MHC molecules while position 5, 6, and 8 will involve in the interaction with the receptor protein. So in this case, i shall specific the active residue of peptide to be 5, 6 and 8 ?

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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:** [September 3, 2025, 12:17pm UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877/4 "2025-09-03T12:17:17Z")

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In principle yes, but the peptide will not be recognized on its own but in the context of the MHC molecule - so you should model the full thing

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**Author:** ![Eugeneng991031](https://avatars.discourse-cdn.com/v4/letter/e/8dc957/32.png) [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\
**Post date:** [September 4, 2025, 12:59am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877/5 "2025-09-04T00:59:31Z")

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Noted with thanks, prof. Let’s say if i just wanna dock the peptide with NKG2A/CD94, will AutoDock Vina be a more suitable tool compared to HADDOCK due to difference in algorithm ?

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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:** [September 4, 2025, 6:16am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877/6 "2025-09-04T06:16:05Z")

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Whatever works best for you…

In HADDOCK you can define restraints to target the docking.