Carbohydrate Structure DataBase

This database aims at provision of structural, bibliographic, taxonomic, NMR spectroscopic and other information on glycan and glycoconjugate structures of prokaryotic, plant and fungal origin. It has been merged from the Bacterial and Plant&Fungal Carbohydrate Structure Databases (BCSDB+PFCSDB). It serves as a platform for multiple glycoinformatic studies and web tools. The key points of this projectc are:

The main source of data is retrospective literature analysis. About 20% of data were imported from CCSD (Carbbank, University of Georgia, Athens; structures published before 1996) with subsequent manual curation and approval. The current coverage is displayed in red on the top of the left menu. The time lag between the publication of new data and their deposition in CSDB is ~1 year.

In the scope of bacterial carbohydrates, CSDB covers nearly all structures published up to 2017. Prokaryotic, plant and fungal means that a glycan was found in the organism(s) belonging to these taxonomic domains or was obtained by modification of those found in these organisms. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds in which at least one residue is a sugar or its derivative, except DNA/RNA.

Besides structures, the database includes bibliography, abstracts, keywords, biological source data up to strains, methods used to elucidate structures, NMR signal assignment and other information. More details are available at the data submission page and in the database schema.

You can search the database by IDs, bibliographic data and keywords, biological source, structural fragments and NMR data. The substructure search supports graphic input, structure wizard, selection from library and query language (expert form).

For referencing and acknowledgements, see Credits.

National users/developers are welcome to a dedicated Russian social network group: VK.

Update history

Color code: general, feature, content update

2018 Project deployment on a new server hardware; performance increase. The web-addresses remained intact.
Selection of residues using SNFG icon map in structure wizard Link
Support of CAZY families in glycosyltransferase search and display
Coverage on Bacteria expanded up to 2017
Coverage on Fungi expanded up to 2010
Built-in support for GlycoCT and update of the RDF feed
Incorporation of SugarSketcher instead of GlycanBuilder Link
Output of Glytoucan IDs whenever a matching CSDB record is displayed
Added predicted glycosyltransferase activities for E. coli up to 2018
2017 Native engine for the generation of atomic coordinates and JSMol visualization of 3D modelsLink
Export to SMILES and display of structural formulas in record display pages and in structure translator Link
Threefold performance increase on search requests and elimination of white screen on long queries
Export to WURCS in the RDF feed, and in structure translator Link
Coverage on Bacteria expanded up to 2016
2016 New NMR-based structure prediction module (GRASS) Link
Achieved close-to-full coverage on A. thaliana and E. coli glycosyltransferases with experimentally confirmed functions
Glycosyltransferase subdatabase launched Link
Flexible completeness and molecule type filters in structureLink and compositionLink search
Major update to multiple Help sections and Examples of usageLink
Improvements, interactive help, and bug fixes in structure search formLink
Coverage on Bacteria expanded up to 2015
Correction of data errors for Bacteria (2000-2014)
2015 Graphic representation of structures using SNFG (Essentials of Glycobiology ver. 3) (extension of so called "CFG notataion")Link
Front page with quick links to most used operationsLink
Nine step-by-step examples of usageLink
2D NMR simulationLink
Coverage on Prokaryotes expanded up to 2014
Coverage on Fungi expanded up to 2005
Statistical 1H NMR simulationLink
Manual verification and re-annotation of data on Bacteria (2007-2013)
2014 Dendrogram drawing/export feature in taxon clustering toolLink
Coverage on Plants and Fungi expanded up to 1997
Import and re-annotation of Carbbank (Plants & Fungi)
Merged CSDB release
Taxonomical domain filter in all types of search
Taxon clustering tool based on glycome similaritiesLink
A tool to gather coverage statistics for given taxaLink
Coverage on Fungi expanded up to 2001
Coverage on Prokaryotes expanded up to 2013
"Report data error" link in every displayed recordLink
2013 Plant&Fungal CSDB release
Statistical and hybrid 13C NMR simulationLink
A tool to study mono- and dimeric fragment distribution among taxaLink
Greek character, apostrophe and quote support in trivial names, Subst aliases and aglycones
Coverage on Prokaryotes expanded up to 2012
Support for hybrid organisms in taxonomic annotations
Cross-linking of monomers to MonosaccharideDB
Updates to monomeric residue subdatabase to handle residues abundant more than 20 times (in structures from all domains)
Updates to linear structure encoding language to support carbon-carbon linkages and apostrophed linkage positions
2012 Topology generatorLink
RDF feed and exportLink
NMR based structure ranking (β)Link
Coverage on Prokaryotes expanded up to 2011
Interface to translate and pass structures to GLYCAM for the geometry predictionLink
Updates to dump-based import, which can detect ~200 types of errors, and correct ~40 types.
2011 Composition searchLink
Full-text filter in structural searchLink
Monomeric residue subdatabase interfaceLink
Help, tutorials, annotators' reference and technical documentation
A tool for translation of structures to and from GlycoCTLink
Coverage on Prokaryotes expanded up to 2010
NMR signal searchLink
Storage of data on taxon renaming or remapping, and corresponding updates in the display of taxa.
2010 Bacterial CSDB release
Empirical 13C NMR simulationLink
Incorporation of graphical GlycanBuilderLink
Coverage on Prokaryotes expanded up to 2009
National character support in Bibliographic searchLink
Widespread structure library in structure input formLink
Host organism and NCBI TaxID filters in Taxonomic searchLink
Structure parser and error detector for annotatorsLink
Generator of templates for annotators, including NMR-templatesLink
Updates to linear structure encoding language to support alternative branches, non-stoichiometrical constituents, unknown configurations and linkage positions, residue superclasses
2005-2009 Import and re-annotation of Carbbank (Bacteria, Archaea & Protista)
Combining, intersection and negation of search queries
Basic search modes
Administrative interface
Data submissionLink, importLink and exportLink
SOAP API and integration with GLYCOSCIENCES.deLink
User feedback formLink
Start of collecting data
Linear structure encoding languageLink
Architectural studiesLink