Carbohydrate Structure Database
Carbohydrate Structure Database is a free curated database and service platform in glycoinformatics, launched in 2005 by a group of Russian scientists from, Russian Academy of Sciences. CSDB stores published structural, taxonomical, bibliographic and NMR-spectroscopic data on natural carbohydrates and carbohydrate-related molecules.
Overview
The main data stored in CSDB are carbohydrate structures of bacterial, fungal, and plant origin. Each structure is assigned to an organism and is provided with the link to the corresponding scientific publication, in which it was described. Apart from structural data, CSDB also stores NMR spectra, information on methods used to decipher a particular structure, and some other data.CSDB provides access to several carbohydrate-related research tools:
- Simulation of 1D and 2D NMR spectra of carbohydrates.
- Automated NMR-based structure elucidation.
- Statistical analysis of structural feature distribution in glycomes of living organisms
- Generation of optimized atomic coordinates for an arbitrary saccharide and subdatabase of conformation maps.
- Taxon clustering based on similarities of glycomes
- Glycosyltransferase subdatabase
History and funding
Until 2015, and databases existed in parallel. In 2015, they were joined into the single . The development and maintenance of CSDB have been funded by,,,, and .Data sources and coverage
The main sources of CSDB data are:- Scientific publications indexed in the dedicated citation databases, including and .
- CCSD database.
As of 2017, the coverage on bacteria and archaea is ca. 80% of carbohydrate structures published in scientific literature The time lag between the publication of relative data and their deposition into CSDB is about 18 months. Plants are covered up to 1997, and fungi up to 2012.
CSDB does not cover data from the animalia domain, except unicellular metazoa. There is a number of dedicated databases on animal carbohydrates, e.g. or .
CSDB is reported as one of the biggest projects in glycoinformatics. It is employed in structural studies of natural carbohydrates and in glyco-profiling.
The content of CSDB has been used as a data source in other glycoinformatics projects.
Deposited objects
- Molecular structures of glycans, glycopolymers and glycoconjugates: primary structure, aglycon information, polymerization degree and class of molecule. Structural scope includes molecules composed of residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds, in which at least one residue is a monosaccharide or its derivative.
- Bibliography associated with structures: imprint data, keywords, abstracts, IDs in bibliographic databases
- Biological context of structures: associated taxon, strain, serogroup, host organism, disease information. The covered domains are: prokaryotes, plants, fungi and selected pathogenic unicellular metazoa. The database contains only glycans originating from these domains or obtained by chemical modification of such glycans.
- Assigned NMR spectra and experimental conditions.
- Glycosyltransferases associated with taxons: gene and enzyme identifiers, full structures, donor and substrates, methods used to prove enzymatic activity, trustworthiness level.
- References to other databases
- Other data collected from original publications
- Conformation maps of disaccharides derived from molecular dynamics simulations.