Glyconvert – The Portal for Conversion Glycoinformatics Formats to General-Purpose Molecular Formats

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1st EuroCarb Young Researcher (ECYR) Workshop

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Mini symposium: Glycobiology at the LUMC and beyond

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Glyconvert – The Portal for Conversion Glycoinformatics Formats to General-Purpose Molecular Formats

Pavla Suchánková 1,2 , Radka Svobodova 1,2 , Frederique Lisacek 3,4

1 NCBR Masaryk University Brno, Kamenice 753/5, 625 00 Brno-Bohunice, Czech Republic, 2CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, 625 00 Brno-Bohunice, 3 Swiss Institute of Bioinformatics, CUI - Battelle - bâtiment A, Route de Drize 7, 1227 Geneva, , 4 University of Geneva, CUI - Battelle - bâtiment A, Route de Drize 7, 1227 Geneva,

Carbohydrates are important biomolecules which play a significant role in cell-cell recognition and other key biological processes. Thanks to high-performance structure determination methods, we have nowadays available a huge amount of biomolecular structures (including saccharides). The glycoinformatics databases are essential for storing specific knowledge about glycans because general-purpose databases do not have enough capacity and resources for preservation all the interesting information. These structures are archived in databases such as Unicarb-DB [1] and Glyconnect [2], where their structures are stored in GlycoCT format [3], which was developed for description of saccharide molecules. The GlycoCT format is useful mainly in machine processing and can be easily generated from the SNFG symbolic representation by SugarSketcher [4], but it is not easy to read by humans. Other structural formats are more appropriate for human processing, e.g. the modified IUPAC condensed in linear form; however, the representation of a molecule in this format may not be unique.

An important challenge of current glycobioinformatics is to combine the advantages of the human-readable and machine-readable format. In this work we address this challenge by implementing a tool for translation between these two formats. Additionally, we want to allow translation into general-purpose structural molecular formats such as InChI, InChIKey, SMILES. This will enable simple searches in common databases that can contain interesting and useful glycan information, e.g. CFG, PubChem [5], ChEBI [6].

Hayes CA, Karlsson NG, Struwe WB, Lisacek F, Rudd PM, Packer NH, Campbell MP. UniCarb-DB: a database resource for glycomic discovery. Bioinformatics. 2011, 27(9), 1343-4.

Glyconnect, Glyconnect, Proteome Informatics Group of SIB, Swiss Institute of Bioinformatics, https://glyconnect.expasy.org/

Herget S, Ranzinger R, Maass K, Lieth CW. GlycoCT—a unifying sequence format for carbohydrates. Carbohydrate Research. 2008, 343(12), 2162-2171.

Alocci D, Suchánková P, Costa R, Hory N, Mariethoz J, Svobodová R, Toukach P, Lisacek F, 2018. SugarSketcher: Quick and Intuitive Online Glycan Drawing. Molecules. 23(12). DOI: 10.3390/molecules23123206. ISSN 1420-3049.

Sunghwan K, Thiessen PA, Bolton EE, et al. PubChem Substance and Compound databases. Nucleic Acids Research. 2016, 44(D1), D1202-D1213.

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Leiden University / Leiden Institute of Chemistry lic.leidenuniv.nl

European Carbohydrate Organisation

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