GLYCAM-Web | Utilities for molecular modeling of carbohydrates

Glycosylated SARS-Cov-2 Spike Protein

The glycans (biantennary LacNAc N-glycans) are shown in dark magenta, the protein trimer as ribbons. The protein 3D structure is the Swiss-Model homology model, which is based on PDBID 6VSB. The glycans were built using GLYCAM-Web. There are 18 glycans per protomer, which comprise ~20% of the mass of the spike protein. Coordinates can be downloaded here.
If you use the coordinates, we request that you cite this publication.
Generate and display 3D structures of the expected shapes of a glycan and download files for viewing offline or for use in other modeling applications, such as for performing MD simulations with AMBER.

If you have access to a crystal structure of a carbohydrate bound to a protein, this tool will use that single co-complex as a basis for predicting which other similar glycans are also likely to bind to the same protein.

This tool facilitates searching for glycans and carbohydrates in the Protein Data Bank (PDB).

If you have access to a 3D structure of your antibody (Fab or Fv domain), this tool will predict the 3D structure of its complex with an oligosaccharide antigen.

If you have access to a 3D structure of your protein, this tool allow you to attach glycans and generate a representative model of the glycoprotein. You can view or download the coordinates, as well as predict the influence of the glycans on the accessibility of the protein surface.

Coming soon! This tool detects and quantifies any likely errors in a glycan 3D structure.

Coming soon! This tool predicts NMR scalar J-couplings and NOE intensities and inter-proton distances for a given glycan structure.