Hi, I’m trying to dock a smaller subunit of a protein to a bigger one. This partly involves the formation of a disulphide bond between residues on either protein (known through biochemical experiments). I tried to dock the proteins keeping an UIR for the two cysteine residues in the hope it would form the disulphide bond but this didn’t work. Naturally, I would think this is a hard thing for HADDOCK to do so I was wondering if there was anything else I could do to specify that a disulphide bond must form between the two structures when I dock.
The disulphide bond will indeed not be created, but you can define instead distance restraints to force the two CYS to come close in space.
This is a bit similar to the docking of covalent ligands which we describe in the following tutorial:
You would have to adapt the example to link the two SG atoms. Also change the residue name of the two cysteine to CYC, which uses a reduced van der Waals radius of the sulphur to allow for a shorted distance between those.