Show simple item record

dc.contributor.authorJo, Sunhwan
dc.contributor.authorSong, Kevin C.
dc.contributor.authorDesaire, Heather
dc.contributor.authorMacKerell, Alexander D., Jr.
dc.contributor.authorIm, Wonpil
dc.date.accessioned2017-05-22T18:56:45Z
dc.date.available2017-05-22T18:56:45Z
dc.date.issued2011-11-15
dc.identifier.citationJo, S., Song, K. C., Desaire, H., MacKerell, A. D., & Im, W. (2011). Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins. Journal of Computational Chemistry, 32(14), 3135–3141. http://doi.org/10.1002/jcc.21886en_US
dc.identifier.urihttp://hdl.handle.net/1808/24266
dc.descriptionThis is the peer reviewed version of the following article: Jo, S., Song, K. C., Desaire, H., MacKerell, A. D., & Im, W. (2011). Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins. Journal of Computational Chemistry, 32(14), 3135–3141. http://doi.org/10.1002/jcc.21886, which has been published in final form at http://doi.org/10.1002/jcc.21886. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.en_US
dc.description.abstractUnderstanding 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 CHARMMGUI, 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.en_US
dc.publisherWileyen_US
dc.subjectMolecular Dynamicsen_US
dc.subjectElectrostatic Surfaceen_US
dc.subjectMembraneen_US
dc.subjectVisualizationen_US
dc.titleGlycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteinsen_US
dc.typeArticleen_US
kusw.kuauthorJo, Sunhwan
kusw.kuauthorSong, Kevin C.
kusw.kuauthorDesaire, Heather
kusw.kuauthorIm, Wonpil
kusw.kudepartmentMolecular Biosciencesen_US
kusw.kudepartmentChemistryen_US
dc.identifier.doi10.1002/jcc.21886en_US
dc.identifier.orcidhttps://orcid.org/0000-0002-4104-6473
kusw.oaversionScholarly/refereed, author accepted manuscripten_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US
dc.identifier.pmidPMC3188666en_US
dc.rights.accessrightsopenAccess


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record