New Tools for Finding Glycans in the PDB & Using the Information to Model 3D Structures of Glycans and GlycoProteins

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 (www.glycam.org) greatly simplifies searching for and retrieving carbohydrate containing structures in the PDB.For more information go tohttps://meetings...
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