I have seen a couple references to this, but I’m not sure the best way to go about it. I don’t think I should set up heparin as a ligand, which I have done with a simple DP4. It seems as though I should link glycans but not sure of the best way to go about it? I didn’t see a lecture file based on the glycan docking but maybe I am missing one.
Hi,
Setting up heparing as a ligand is likely the best choice, as it is typically highly sulfated and we currently have no support for sulfonated glycans (the list of supported ones is here HADDOCK Web Server - Settings). See for example this topic Recognition problem after glycan sulfation
For supported glycans there is a new tutorial describing the best docking protocol (in that case using HADDOCK3): Protein-glycan modelling tutorial using a local version of HADDOCK3 – Bonvin Lab
Cheers,
Marco