Carbohydrate Structure Database (CSDB)

NAR Molecular Biology Database Collection entry number 1904
Toukach, Philip; Egorova, Ksenia

Database Description

Carbohydrate Structure Database (CSDB) stores published data on glycans and glycoconjugates of bacterial, archaean, plant and fungal origin.

It provides data on structures, bibliography, taxonomy, 1H and 13C NMR spectrum assignment, methods used for structure elucidation, cross-references, and other information. As of 2015, it contains ca. 17,100 glycan structures from ca. 7800 organisms published in ca. 6500 articles. The coverage on bacteria is closed to complete up to 2014, and the coverage on fungi is close to complete up to 2005. Most data come from manual curation based on retrospective literature analysis. A part of structures published before 1996 was imported from the CarbBank database, appended with missing data and verified manually against the original publications with error correction. Main features of CSDB are:

(1) regular updates aiming at high coverage, ca. 1000 new records are added annually;

(2) high data quality achieved by automated and manual expert verification;

(3) manually verified bibliographic, taxonomic, and NMR spectroscopic annotations;

(4) automated data exchange with numerous other databases using dedicated formats and Resource Description Framework;

(5) free access on the Internet

CSDB is supplied with additional tools for empirical or database-driven 13C and 1H NMR spectrum simulation (including 2D NMR), NMR-based structure ranking, statistics on coverage and distribution of structural fragments among taxa, and clustering of taxa based on similarities in their glycomes.

Subcategory: Carbohydrates

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