GLYCAM/WEB's Glycoprotein web-tool may be used to build oligosaccharides and attach them to a proteins to form either O- or N-linked glycoproteins. This is achieved through the following sequence:

• Upload a protein structure in standard PDB format. The best results are obtained when non-protein (HETATM) coordinates are removed prior to uploading.
• Use the point-and-click Carbohydrate Builder GUI to build the glycan
• Use the Glycoprotein builder to select the glycosylation site and attach the glycan
• Continue adding more glycan chains or finish and download the pdb structure.

For those interested in performing energy minimization or molecular dynamics simulation of their glycoprotein with AMBER , options are presented to solvate their model with water and download the necessary additional files (coordinate and topology).

It should be noted that under physiological conditions oligosaccharides are frequently highly flexible, and a single static structure is an incomplete model for both glycans and glycoproteins.

For this reason, the user is encouraged to employ molecular dynamics simulations to develop a more complete understanding of the spatial and dynamic properties of their system.