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Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and... Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM‐GUI, http://www.charmm‐gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three‐dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N‐/O‐glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM‐GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Computational Chemistry Wiley

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins

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References (35)

Publisher
Wiley
Copyright
Copyright © 2011 Wiley Periodicals, Inc.
ISSN
0192-8651
eISSN
1096-987X
DOI
10.1002/jcc.21886
pmid
21815173
Publisher site
See Article on Publisher Site

Abstract

Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM‐GUI, http://www.charmm‐gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three‐dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N‐/O‐glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM‐GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

Journal

Journal of Computational ChemistryWiley

Published: Nov 15, 2011

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