Glycan modeling is performed with the Carbohydrate framework within the Rosetta suite 1,2. Existing glycan structures can be sampled to find the more stable conformations, or glycan chains can be build from scratch. Proteins structures can be scanned to existing glycosylation sites (according to the sequon NxS/T) or they can be re-designed for the insertion of new glycosylation sites. More info on the Rosetta Carbohydrate framework can be found at:
https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans
Relevant Bibliography:
[1] Labonte, J. W., Adolf-Bryfogle, J., Schief, W. R. & Gray, J. J. Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures. J. Comput. Chem. 38, 276–287 (2017).
[2]
Frenz, B. et al. Automatically Fixing Errors in Glycoprotein Structures with Rosetta. Struct. Lond. Engl. 1993 27, 134-139.e3 (2019).