Introducing a mutation in a protein-protein docking

HADDOCK
1

Greetings haddock team,

I would like to introduce a single amino acid variant in a protein domain structure from pdb and then perform a protein-protein docking using this structure.
On your guide it says that we can introduce a mutation in an input protein structure by simply edit the PDB file and change the residue name of the amino-acid you want to modify.
I wanted to ask you where in the pdb file I have to change the residue name? In each atom row of the aminoacid that I want to change?
Can’t that change modify the structure of my protein? And in that case will that be managed by haddock?

Thank you

2

Yes

It can of course, but this would only happen during the flexible refinement.
And it only makes sense to introduce mutations in the interface.

Otherwise you should use another way of introducing the mutation and possible run some MD.

HADDOCK will build any missing atom.

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