Paper Info
Title
Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.
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. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 3135-3141, 2011
Year
DOI
Venue
2011
10.1002/jcc.21886
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
molecular dynamics,electrostatic surface,membrane,visualization
Glycosidic bond,Glycosylation,Glycobiology,Biochemistry,Glycoprotein,Chemistry,Molecular dynamics,Protein Data Bank (RCSB PDB),Glycan,Protein structure
Journal
Volume
Issue
ISSN
32
14
0192-8651
Citations 
PageRank 
References 
8
0.59
12
Authors
5
Name
Order
Citations
PageRank
Sunhwan Jo113413.08
Kevin C Song2231.59
Heather Desaire380.59
Alexander D. MacKerell Jr.4104498.55
Wonpil Im513221.26