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

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

Copyright © 2011 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 32(2011), 14 vom: 15. Nov., Seite 3135-41
1. Verfasser: Jo, Sunhwan (VerfasserIn)
Weitere Verfasser: Song, Kevin C, Desaire, Heather, MacKerell, Alexander D Jr, Im, Wonpil
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2011
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Carbohydrates Glycoproteins
Beschreibung
Zusammenfassung:Copyright © 2011 Wiley Periodicals, Inc.
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
Beschreibung:Date Completed 30.01.2012
Date Revised 16.03.2022
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.21886