Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.

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TitleGlycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.
Publication TypeJournal Article
Year of Publication2011
AuthorsJo, S, Song, KC, Desaire, H, Mackerell, AD, Im, W
JournalJ Comput Chem
Volume32
Issue14
Pagination3135-41
Date Published2011 Nov 15
ISSN1096-987X
KeywordsAlgorithms, Carbohydrates, Glycoproteins, Models, Molecular, Molecular Dynamics Simulation, Static Electricity
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.

DOI10.1002/jcc.21886
Alternate JournalJ Comput Chem
PubMed ID21815173
PubMed Central IDPMC3188666
Grant ListR01 GM070855 / GM / NIGMS NIH HHS / United States
R01-GM070855 / GM / NIGMS NIH HHS / United States
R01 GM103547 / GM / NIGMS NIH HHS / United States
P20 RR017708 / RR / NCRR NIH HHS / United States
P20 RR-17708 / RR / NCRR NIH HHS / United States
P20 RR017708-10 / RR / NCRR NIH HHS / United States
R01 RR026061-03 / RR / NCRR NIH HHS / United States
R01-RR026061 / RR / NCRR NIH HHS / United States
R01 GM070855-07 / GM / NIGMS NIH HHS / United States
R01 RR026061 / RR / NCRR NIH HHS / United States