BACTERIAL, PLANT, AND FUNGAL CARBOHYDRATE STRUCTURE DATABASES: DAILY USAGE

Ph.V. Toukach, K.S. Egorova

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

KEYWORDS: BCSDB, CSDB, carbohydrate, database, carbohydrate structure, bacterial carbohydrate, archaeal carbohydrate, plant carbohydrate, fungal carbohydrate, bibliography, taxonomy, NMR, NMR spectrum prediction, glycan description, glycoinformatics

chapter in "Glycoinformatics", series: Methods in Molecular Biology, v. 1273.
Eds.: T. Lütteke, M. Frank,
Springer New York, 2015, ch. 5, pp. 55-85.
Print ISBN 978-1-4939-2342-7, Online ISBN 978-1-4939-2343-4

DOI: 10.1007/978-1-4939-2343-4_5


Natural carbohydrates play important roles in living systems and therefore are used as diagnostic and therapeutic targets. The main goal of glycomics is systematization of carbohydrates and elucidation of their role in human health and disease. The amount of information on natural carbohydrates accumulates rapidly, but scientists still lack databases and computer-assisted tools needed for orientation in the glycomic information space. Therefore, freely available, regularly updated and cross-linked databases are demanded. Bacterial Carbohydrate Structure Database (Bacterial CSDB) was developed for provision of structural, bibliographic, taxonomic, NMR spectroscopic, and other related information on bacterial and archaeal carbohydrate structures. Its main features are: (1) coverage above 90%; (2) high data consistence (above 90% of error-free records); and (3) presence of manually verified bibliographic, NMR spectroscopic, and taxonomic annotations. Recently, CSDB has been expanded to cover carbohydrates of plant and fungal origin. The achievement of full coverage in the plant and fungal domains is expected in the future. CSDB is freely available on the Internet as a web service at http://csdb.glycoscience.ru. This chapter aims at showing how to use CSDB in your daily scientific practice.


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