Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans

Carbohydrate Research
Shinichiro TsuchiyaHisashi Narimatsu

Abstract

GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) was proposed during the early stages of the GlyTouCan project. GlyTouCan uses WURCS as its base representation for glycans because existing formats were insufficient in their flexibility to represent any and all glycans universally. Therefore, in order to obtain WURCS strings for existing or new glycan structures, conversion tools or glycan structure editors that can export WURCS became necessary. GlycanBuilder was an obvious choice to extend due to its wide usage by the community. However, GlycanBuilder was limited because it was originally developed to support mammalian glycans. It also did not support the newly proposed monosaccharide symbol standard called Symbol Nomenclature for Glycans (SNFG). Therefore in this work, we implemented a new version of GlycanBuilder to greatly increase its usability. The glycan rendering system was refactored so that cyclic glycans, nested repeating units, monosaccharide compositions and cross-linked glycan structures can be represented. Both import and export utilities for WURCS were also implemented and SN...Continue Reading

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Citations

Sep 20, 2017·Glycobiology·Michael TiemeyerKiyoko F Aoki-Kinoshita
Jun 12, 2019·Glycobiology·Sriram NeelameghamUNKNOWN SNFG Discussion Group
Oct 24, 2019·BMC Bioinformatics·Thomas Lemmin, Cinque Soto
Dec 20, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Davide AlocciFrédérique Lisacek
Oct 22, 2020·Beilstein Journal of Organic Chemistry·Kanhaya LalSerge Perez
Oct 22, 2020·International Journal of Molecular Sciences·Sofya I Scherbinina, Philip V Toukach
Jun 3, 2021·Biomolecules·Giulia PaiardiMarco Rusnati
Jul 7, 2018·Chemical Reviews·Carmanah D HunterChristopher W Cairo
Sep 2, 2021·EMBO Molecular Medicine·René G FeichtingerSaskia B Wortmann
Sep 7, 2021·Frontiers in Bioengineering and Biotechnology·Johannes RuhnauUdo Reichl
Oct 2, 2021·Journal of Chemical Information and Modeling·Andrei Y Bochkov, Philip V Toukach

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