# Mutagenesis/Substitution introduction with HADDOCK

**URL:** <https://ask.bioexcel.eu/t/mutagenesis-substitution-introduction-with-haddock/4426>\
**Category:** HADDOCK\
**Created:** [July 24, 2023, 10:10am UTC](https://ask.bioexcel.eu/t/mutagenesis-substitution-introduction-with-haddock/4426 "2023-07-24T10:10:28Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Marija](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marija/32/278_2.png) [@Marija](https://ask.bioexcel.eu/u/Marija)\
**Post date:** [July 24, 2023, 10:10am UTC](https://ask.bioexcel.eu/t/mutagenesis-substitution-introduction-with-haddock/4426/1 "2023-07-24T10:10:28Z")

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Hello everyone,

I introduced mutations into my protein with HADDOCK by just removing all atoms up to C-beta, changing the name of the residue, and submitting to the refinement.  
I have a question how HADDOCK introduces the substitution/mutation, does it use Molprobity’s rotamers library or something else? Is there a publication which can be cited, if the mutagenesis with HADDOCK was used?

With best regards,  
Marija

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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:** [July 24, 2023, 11:45am UTC](https://ask.bioexcel.eu/t/mutagenesis-substitution-introduction-with-haddock/4426/2 "2023-07-24T11:45:07Z")

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No specific reference.

It is a CNS protocol that basically freeze the known atoms, randomly places the unknown ones around the residue, and rebuilds the missing parts in a simulated annealing protocol in which the force field terms are slowly increased (bonds, angles, dihedrals…)

I.e. no use of any rotameric states