New Tools for Finding Glycans in the PDB & Modeling 3D Structures of Glycans & GlycoProteins



Interested in glycan/glycoprotein 3D structures?
This free webinar will present tools to help find glycans in the Protein Data Bank and model their structures. The focus will be on SARS-CoV-2.

1:30-3:30 p.m., EDT
Registration is FREE:

Registration Link
Video Cast Link
Please feel free to send any questions or feedback to:


Session I

1:30 p.m., EDT

Introduction by Dr. Woods

David Montgomery: Finally, a New Approach to Annotating and Finding Carbohydrates in the PDB

Topics Covered:

  • A simple uniform representation for oligosaccharides in the PDB – translating chaos to order
  • When does a carbohydrate stop being a carbohydrate?
  • What to do with errors and uncertainties?
  • GlyFinder, an awesome new way to search the PDB for all structures glyco
  • Live demo with audience participation
  • Beyond point-and-click: tools for glyco informaticians

Session II

2:15 p.m., EDT

Dr. Lachele Foley: Easy Tools for Modeling 3D Carbohydrate Structures

Topics Covered:

  • Live demo with audience participation
  • Do the models match the PDB structures? Should they?

Slides including links to websites referenced during the talk:

2:35 p.m., EDT

Dr Al French:   Case study demonstrating the GlyFinder tool and comparing to quantum mechanical data

  • Case study in the use of GlyFinder

Slides from the talk:  Al_French_Glyfinder_Presentation

Session III

2:45 p.m., EDT

Dr. Oliver Grant: How to generate scientifically meaningful (and beautiful) models of glycoproteins

Topics Covered:

  • A structural biologists conundrum – how to integrate glycomics data into 3D structures?
  • Case study SARS CoV-2 Spike glycoprotein
  • Science meets art (VMD images)
  • Removing the tedium: really cool automated tools – coming soon!

VMD Tutorial


Glycans play a critical role in nearly all aspects of biology, ranging from how our bodies recognize and fight viruses and bacteria to how proteins are moved throughout our cells to perform different tasks. The Common Fund’s Glycoscience program (CF-GSP) is creating new resources, tools, and methods to make the study of glycans (sugars) more accessible to the broader research community. The Protein Data Bank (PDB) contains more than 160,000 3D structures of biological macromolecules 20% of which contain carbohydrates as ligands or as chemical modifications. Unfortunately, much of the PDB’s carbohydrate structural data contains errors and/or inconsistencies in annotation. As part of a broad carbohydrate remediation initiative at the wwPDB, Dr. Robert Woods (with support from the CF-GSP) has developed a software tool “GlyFinder” to both address errors in deposited coordinates, and to search for carbohydrate structures in the PDB. “Glyfinder” checks the internal consistency of the 3D structures of carbohydrates, converts the ad hoc nomenclature to a residue-based standard, parses the deposited coordinates of glycans into monosaccharide-based oligosaccharide chains, and provides a simple linear representation for the oligosaccharide sequence. In addition, the “GlyFinder” search interface implemented at GLYCAM-Web ( greatly simplifies searching for and retrieving carbohydrate containing structures in the PDB.

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