Author Archives: stefan

Visualizing PDB Files Containing Glycans

Carbohydrates in the PDB and VMD For reasons that are mostly historical, carbohydrates are currently not treated well in non-specialist databases such as the PDB or in visualization software such as VMD.  Efforts are underway to improve the situation.  In the meantime, this exercise will explain some of the problems, and offer some ways to […]

Glycosylating Erythropoietin Using 1BUY.pdb

Overview In this exercise, we will: Download a PDB structure of a mutated protein. In its native state, the protein is glycosylated, and it does not perform its functions properly without at least some of the glycosylation. Use the text editor and the utilities at GLYCAM-Web to change the mutated residues back to the natural […]

Introduction to GLYCAM-Web

Overview GLYCAM-Web provides tools to facilitate molecular modeling of oligosaccharides and larger molecular structures containing glycans.  Type ‘’ (or ‘’) to go there.  You should see a page looking like the one just below.   Once there, click on 3D Structure Prediction Tools, the gray tab on the left near the top.  You should now […]