[AMBER] GlycoTools Webinar tomorrow

From: Lachele Foley <lf.list.gmail.com>
Date: Thu, 13 Aug 2020 10:34:28 -0400

Hi folks!

Our group is giving a webinar for the NIH tomorrow, 1:30-3:30 PM
US-Eastern time. We'll be presenting tools to find carbohydrates in
the PDB, giving a little overview of abilities at GLYCAM-Web and
showing ways to represent glycoproteins. See below for details.

Registration is FREE: https://meetings.nigms.nih.gov/?ID=29099

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.

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

1:30-3:30 p.m., EDT


Introduction by Dr. Woods

Session I., Finally, a New Approach to Annotating and Finding
Carbohydrates in the PDB (45 minutes)

David Montgomery

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., Easy Tools for Modeling 3D Carbohydrate Structures (30 minutes)

Dr. Lachele Foley

Topics Covered:

live demo with audience participation
do the models match the PDB structures? Should they?
case study (Dr. Al French) demonstrating the GlyFinder tool and
comparing to quantum mechanical data

Session III., How to generate scientifically meaningful (and
beautiful) models of glycoproteins (45 minutes)

Dr. Oliver Grant

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

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Aug 13 2020 - 08:00:03 PDT
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