# Disulfide bonds: How to add them in HADDOCK 3?

**URL:** <https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997>\
**Category:** HADDOCK\
**Tags:** haddock\
**Created:** [February 3, 2026, 3:46am UTC](https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997 "2026-02-03T03:46:15Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Hoa\_Thanh\_Le](https://avatars.discourse-cdn.com/v4/letter/h/5f9b8f/32.png) [@Hoa\_Thanh\_Le](https://ask.bioexcel.eu/u/Hoa_Thanh_Le)\
**Post date:** [February 3, 2026, 3:46am UTC](https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997/1 "2026-02-03T03:46:15Z")

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Hello,

I want to dock a peptide to a protein with disulfide bonds, using HADDOCK 3. I would like to ask how to tell the program which Cysteine residues will form disulfide bonds before docking?

Best regards,

Hoa

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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 3, 2026, 4:07am UTC](https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997/2 "2026-02-03T04:07:38Z")

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Do you mean that disulphide bonds are formed between the protein and the peptide?

If this is the case you should define a few distance restraints between the CYS sulphur atoms.

If you rather refer to the disulphide bonds within your protein, those are automatically detected.

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**Author:** ![Hoa\_Thanh\_Le](https://avatars.discourse-cdn.com/v4/letter/h/5f9b8f/32.png) [@Hoa\_Thanh\_Le](https://ask.bioexcel.eu/u/Hoa_Thanh_Le)\
**Post date:** [February 3, 2026, 7:04am UTC](https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997/3 "2026-02-03T07:04:33Z")

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Thank you for your information. I mean the disulphide bonds within my protein.

It’s good that they are automatically detected. But can there be cases where two independent, non-bonded sulfur atoms happen to be close to each other, but HADDOCK 3 still forms a disulphide bond between them? If these cases are possible, is there a way to tell HADDOCK 3 not to add the bond between them?

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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 3, 2026, 8:25am UTC](https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997/4 "2026-02-03T08:25:38Z")

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HADDOCK uses a distance criterion to detect S-S bonds. You can not really turn this off (or you would have to hack some scripts).

But if these are internal and not close to the binding site it won’t matter I would say.

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**Author:** ![Hoa\_Thanh\_Le](https://avatars.discourse-cdn.com/v4/letter/h/5f9b8f/32.png) [@Hoa\_Thanh\_Le](https://ask.bioexcel.eu/u/Hoa_Thanh_Le)\
**Post date:** [February 3, 2026, 8:48am UTC](https://ask.bioexcel.eu/t/disulfide-bonds-how-to-add-them-in-haddock-3/5997/5 "2026-02-03T08:48:02Z")

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Thank you, Mr. Bonvin. Your insight is helping me making decision for my docking project.

I wish you and your team success in developing the rest of the features for HADDOCK 3!