dc.contributor.author | Jo, Sunhwan | |
dc.contributor.author | Song, Kevin C. | |
dc.contributor.author | Desaire, Heather | |
dc.contributor.author | MacKerell, Alexander D., Jr. | |
dc.contributor.author | Im, Wonpil | |
dc.date.accessioned | 2017-05-22T18:56:45Z | |
dc.date.available | 2017-05-22T18:56:45Z | |
dc.date.issued | 2011-11-15 | |
dc.identifier.citation | 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 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/24266 | |
dc.description | This 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.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 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.publisher | Wiley | en_US |
dc.subject | Molecular Dynamics | en_US |
dc.subject | Electrostatic Surface | en_US |
dc.subject | Membrane | en_US |
dc.subject | Visualization | en_US |
dc.title | Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Jo, Sunhwan | |
kusw.kuauthor | Song, Kevin C. | |
kusw.kuauthor | Desaire, Heather | |
kusw.kuauthor | Im, Wonpil | |
kusw.kudepartment | Molecular Biosciences | en_US |
kusw.kudepartment | Chemistry | en_US |
kusw.oanotes | Per SHERPA/RoMEO 5/22/2017: Author's Pre-print: green tick author can archive pre-print (ie pre-refereeing)
Author's Post-print: grey tick subject to Restrictions below, author can archive post-print (ie final draft post-refereeing)
Restrictions: 12 months embargoPublisher's Version/PDF: cross author cannot archive publisher's version/PDF
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Author's pre-print may not be updated with Publisher's Version/PDF
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Non-Commercial
Publisher's version/PDF cannot be used
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If OnlineOpen is available, BBSRC, EPSRC, MRC, NERC and STFC authors, may self-archive after 12 months | en_US |
dc.identifier.doi | 10.1002/jcc.21886 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-4104-6473 | |
kusw.oaversion | Scholarly/refereed, author accepted manuscript | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC3188666 | en_US |
dc.rights.accessrights | openAccess | |