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Carbohydrate Structure Database: current state and recent developments

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Abstract

Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D modeler, NMR simulator, NMR-based structure predictor, and other tools.

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Abbreviations

API:

Application programming interface

CASPER:

Computer-assisted spectrum evaluation of regular polysaccharides

CAZY:

Carbohydrate-active enzyme

COSY:

Correlation spectroscopy

CSDB:

Carbohydrate Structure Database

GLC:

Gas-liquid chromatography

GT:

Glycosyltransferase

GODDESS:

Glycan-optimized database-driven empirical spectrum simulation

GRASS:

Generation, ranking, and assignment of saccharide structures

HMBC:

Heteronuclear multiple bond correlation

HOSE:

Hierarchical organization of spherical environment

HSQC:

Heteronuclear single-quantum coherence

ICD:

International Classification of Diseases

IEDB:

Immune Epitope Database

KEGG:

Kyoto Encyclopedia of Genes and Genomes

MSDB:

Monosaccharide Database

MESH:

Medical subject headings

NLM:

National Library of Medicine

PMID:

PubMed identifier

RDF:

Resource description framework

ROESY:

Rotating frame Overhauser effect spectroscopy

SMILES:

Simplified molecular-input line-entry system

SNFG:

Symbolic nomenclature for glycans

TOCSY:

Total correlation spectroscopy

PDB:

Protein Data Bank

WURCS:

Web3 unique representation of carbohydrate structures

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Acknowledgements

 The author acknowledges all the CSDB team involved in the CSDB product life cycle. The participants are listed at http://csdb.glycoscience.ru/help/credits.html.

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The author declares no funding in 2023-2024.

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  1. N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia

    Philip Toukach

  2. Faculty of Chemistry, National Research University Higher School of Economics, Moscow, Russia

    Philip Toukach

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Published in the topical collection featuring Current Progress in Glycosciences and Glycobioinformatics with guest editors Joseph Zaia and Kiyoko F. Aoki-Kinoshita.

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Toukach, P. Carbohydrate Structure Database: current state and recent developments. Anal Bioanal Chem (2024). https://doi.org/10.1007/s00216-024-05383-w

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