Literature DB >> 23109548

The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments.

David Damerell1, Alessio Ceroni, Kai Maass, Rene Ranzinger, Anne Dell, Stuart M Haslam.   

Abstract

During the EUROCarbDB project our group developed the GlycanBuilder and GlycoWorkbench glycoinformatics tools. This short communication summarizes the capabilities of these two tools and updates which have been made since the original publications in 2007 and 2008. GlycanBuilder is a tool that allows for the fast and intuitive drawing of glycan structures; this tool can be used standalone, embedded in web pages and can also be integrated into other programs. GlycoWorkbench has been designed to semi-automatically annotate glycomics data. This tool can be used to annotate mass spectrometry (MS) and MS/MS spectra of free oligosaccharides, N and O-linked glycans, GAGs (glycosaminoglycans) and glycolipids, as well as MS spectra of glycoproteins.

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Year:  2012        PMID： 23109548     DOI： 10.1515/hsz-2012-0135

Source DB:  PubMed          Journal:  Biol Chem        ISSN： 1431-6730            Impact factor:   3.915


  62 in total

1.  Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

Authors:  Peter D Karp; Mario Latendresse; Suzanne M Paley; Markus Krummenacker; Quang D Ong; Richard Billington; Anamika Kothari; Daniel Weaver; Thomas Lee; Pallavi Subhraveti; Aaron Spaulding; Carol Fulcher; Ingrid M Keseler; Ron Caspi
Journal:  Brief Bioinform       Date:  2015-10-10       Impact factor: 11.622

Review 2.  Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data.

Authors:  Gang Liu; Sriram Neelamegham
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2015-04-13

Review 3.  Recent Advances in the Analysis of Complex Glycoproteins.

Authors:  Stefan Gaunitz; Gabe Nagy; Nicola L B Pohl; Milos V Novotny
Journal:  Anal Chem       Date:  2016-11-23       Impact factor: 6.986

4.  Quantitative Glycomics: A Combined Analytical and Bioinformatics Approach.

Authors:  L Veillon; S Zhou; Y Mechref
Journal:  Methods Enzymol       Date:  2017-01-09       Impact factor: 1.600

Review 5.  Glycosaminoglycanomics: where we are.

Authors:  Sylvie Ricard-Blum; Frédérique Lisacek
Journal:  Glycoconj J       Date:  2016-11-30       Impact factor: 2.916

6.  Differential Fragmentation of Mobility-Selected Glycans via Ultraviolet Photodissociation and Ion Mobility-Mass Spectrometry.

Authors:  Kelsey A Morrison; Brian H Clowers
Journal:  J Am Soc Mass Spectrom       Date:  2017-04-18       Impact factor: 3.109

Review 7.  Using databases and web resources for glycomics research.

Authors:  Kiyoko F Aoki-Kinoshita
Journal:  Mol Cell Proteomics       Date:  2013-01-16       Impact factor: 5.911

8.  Glycan analysis of human neutrophil granules implicates a maturation-dependent glycosylation machinery.

Authors:  Vignesh Venkatakrishnan; Régis Dieckmann; Ian Loke; Harry C Tjondro; Sayantani Chatterjee; Johan Bylund; Morten Thaysen-Andersen; Niclas G Karlsson; Anna Karlsson-Bengtsson
Journal:  J Biol Chem       Date:  2020-07-14       Impact factor: 5.157

9.  Isotopic labeling with cellular O-glycome reporter/amplification (ICORA) for comparative O-glycomics of cultured cells.

Authors:  Matthew R Kudelka; Alison V Nairn; Mohammed Y Sardar; Xiaodong Sun; Elliot L Chaikof; Tongzhong Ju; Kelley W Moremen; Richard D Cummings
Journal:  Glycobiology       Date:  2018-04-01       Impact factor: 4.313

Review 10.  The challenge and promise of glycomics.

Authors:  Richard D Cummings; J Michael Pierce
Journal:  Chem Biol       Date:  2014-01-16
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