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

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

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Air date:	Friday, August 14, 2020, 1:30:00 PM Time displayed is Eastern Time, Washington DC Local
Views:	Total views: 837 (292 Live, 545 On-demand)
Category:	Conferences
Runtime:	01:53:17
Closed captioning:	Check box to display CC outside of the video Note: You can drag the captioning window around and resize it
Description:	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 to https://meetings.nigms.nih.gov/?ID=29099

NLM Title:	New tools for finding glycans in the PDB & using the information to model 3D structures of glycans and glycoproteins / David Montgomery, B. Lachele Foley, Oliver C. Grant.
Author:	Montgomery, David. Foley, B Lachele. Grant, Oliver C. Common Fund Glycoscience Program,
Publisher:
Abstract:	(CIT): 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.
Subjects:	Computer Simulation Databases, Protein Glycoproteins--physiology Imaging, Three-Dimensional Polysaccharides--physiology
Publication Types:	Lecture Webcast

NLM Classification:	QU 83
NLM ID:	101771235
CIT Live ID:	38241
Permanent link:	https://videocast.nih.gov/watch=38241

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