Dear Prof. Bonvin, I tried to dock a glyco-peptide to an antibody using HADDOCK 2.4-web. The result shows that the glycan linkage was broken and each sugar residue was blown out. The glycan structure is Sia-Gal-GalNAc attached to Thr residue of the ligand peptide. Is such glycopeptide supported in HADDOCK 2.4-web? It seems that sugar residue was not recognized by the system and the glycan part was shown as “XXX”. Any information is welcome to get a result. Thanking you in advance.
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