Mutagenesis/Substitution introduction with HADDOCK

HADDOCK
1

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

2

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

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