I have to dock two proteins and confirm the interaction interface. I have two pdb files. One protein is hightly glycosylated. The pdb file defined the glycans and the connection. I used the easy interface of HADDOCK and found it did not consider the glycans and all glycans were pushed outside of the structure. How can I incorporate glycan in the docking?
Thanks
You will need parameter and topology files for the glycans. When using the server, the oligosaccharide will be treated as one residue basically (that’s what PRODRG does). So you should not have overlap in nomenclature and a single residue name
hope this helps
The problem is that the glycans are treated as ligands and won’t be covalently attached to the protein in HADDOCK (we simply don’t have support for this implemented). So if you want to keep your glycans in proper positions, you will have to define a few distance restraints per glycans to the protein.
Your HADDOCK-tools repo on GitHub (https://github.com/haddocking/haddock-tools) does contain a script that allows you to define such restraints. Check the restrain_ligand.py script.
Also important as explained in the previous answer, a glycan should have only a single residue name and non overlapping atom naming.
Thank you so much.
junxia