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:
- High coverage. The coverage for prokaryotes and fungi (up to 2021) is above 80%. Similar coverage for plants (now up to 2000) is expected in the future.
- Data quality. High data quality is achieved by manual curation of original publications assisted by automatic procedures for error control. Errors present in publications are reported and corrected, when possible. Data from other databases are verified on import.
- Detailed annotations. Structural data are supplied with extended bibliography, assigned NMR spectra, taxon identification including strains and serogroups, and other information if available in the original publication.
- Services. CSDB serves as a platform for a number of computational services tuned for glycobiology, such as NMR simulation, automated structure elucidation, taxon clustering, 3D molecular modeling, statistical processing of data etc.
- Integration. CSDB is cross-linked to other glycoinformatics projects and NCBI databases. The data are exportable in various formats, including most widespread encoding schemes and records using GlycoRDF ontology.
- Free web access. Users can access the database for free via its web interface (see Help).
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 1-2 years.
In the scope of bacterial carbohydrates, CSDB covers nearly all structures published up to the previous year. 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: 
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Update history
Color code: general, feature, content update
| 2023 | Added calculation of molecular weight for database or user-input structures  |
| Coverage on Bacteria expanded up to 2022 (full coverage) | |
| Coverage on Plants expanded up to 2000 |
| 2022 | Taxonomic search was adapted to selection of multiple taxa in one query | Every shown structure was mapped to candidate glycosyltransferases for its enzymatic synthesis |
| Coverage on Protista expanded up to 2021 (full coverage) | |
| Launched epitope subdatabase | |
| Coverage on Fungi expanded up to 2021 (full coverage) | |
| Coverage on Bacteria expanded up to 2021 (full coverage) | |
| Added A. baumannii (up to 2021) to the glycosyltransferase database | |
| 2021 | Bacterial and Plant&Fungal databases have been finally merged on interface, content, and ID levels; the ancestor databases have been discontinued |
| Launched aglycon subdatabase | |
| New built-in translator to extended GlycoCT with full support of ALT, REP and NON | |
| Coverage on Fungi expanded up to 2020 (full coverage) | |
| Coverage on Bacteria expanded up to 2020 (full coverage) | |
| Coverage on Plants expanded up to 1999 | |
| 2020 | Launched conformation map subdatabase and conformation explorer |
| Linked enzyme and gene IDs in glycosyltransferase database to KEGG entries and orthologs | |
| Coverage on Bacteria expanded up to 2019 | |
| Achieved close-to-full coverage on S. cerevisiae glycosyltransferases with experimentally confirmed activity | |
| New SNFG-based graphical structure editor | |
| 3D modeller equiped with full JSmol molecular viewer engine, and 3D structures got residue coloring according to SNFG colors | |
| Diseases, organs, tissues and life stages standardized; database entries linked to International classification of diseases (ICD-11) | |
| Coverage on Fungi expanded up to 2015, plus 2017, in-part 2018 | |
| 2019 | Resolving uncertainties in underdetermined structures and export to MOL and PDB in the user interface and in the web API |
| Taxon names are linked to NCBI Lifemap visualizer, when displayed | |
| Coverage on Bacteria expanded up to 2018 | |
| Coverage on Fungi expanded up to 2011, plus 2017 | |
| Extended tools for database annotators, including multifunctional structure checker. | |
| Updates to CSDB Linear notation to support internal repeating sub-parts and SMILES-encoded moieties | |
| 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  | |
| 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 | |
| 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 models |
| Export to SMILES and display of structural formulas in record display pages and in structure translator | |
| 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 | |
| Coverage on Bacteria expanded up to 2016 | |
| 2016 | New NMR-based structure prediction module (GRASS) |
| Achieved close-to-full coverage on A. thaliana and E. coli glycosyltransferases with experimentally confirmed functions | |
| Glycosyltransferase subdatabase launched | |
| Flexible completeness and molecule type filters in structure and composition search | |
| Major update to multiple Help sections and Examples of usage |
|
| Improvements, interactive help, and bug fixes in structure search form | |
| 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 notatat ion") |
| Front page with quick links to most used operations | |
| Nine step-by-step examples of usage | |
| 2D NMR simulation | |
| Coverage on Prokaryotes expanded up to 2014 | |
| Coverage on Fungi expanded up to 2005 | |
| Statistical 1H NMR simulation | |
| Manual verification and re-annotation of data on Bacteria (2007-2013) | |
| 2014 | Dendrogram drawing/export feature in taxon clustering tool |
| 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 similarities | |
| A tool to gather coverage statistics for given taxa | |
| Coverage on Fungi expanded up to 2001 | |
| Coverage on Prokaryotes expanded up to 2013 | |
| "Report data error" link in every displayed record | |
| 2013 | Plant&Fungal CSDB release |
| Statistical and hybrid 13C NMR simulation | |
| A tool to study mono- and dimeric fragment distribution among taxa | |
| 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 CSDB Linear notation to support carbon-carbon linkages and apostrophed linkage positions | |
| 2012 | Topology generator |
| RDF feed and export | |
| NMR-based structure ranking (β) | |
| Coverage on Prokaryotes expanded up to 2011 | |
| Interface to translate and pass structures to GLYCAM for the geometry prediction | |
| Updates to dump-based import, which can detect ~200 types of errors, and correct ~40 types. | |
| 2011 | Composition search |
| Full-text filter in structural search | |
| Monomeric residue subdatabase interface | |
| Help, tutorials, annotators' reference and technical documentation | |
| A tool for translation of structures to and from GlycoCT | |
| Coverage on Prokaryotes expanded up to 2010 | |
| NMR signal search | |
| Storage of data on taxon renaming or remapping, and corresponding updates in the display of taxa. | |
| 2010 | Bacterial CSDB release |
| Empirical 13C NMR simulation | |
| Incorporation of graphical GlycanBuilder | |
| Coverage on Prokaryotes expanded up to 2009 | |
| National character support in Bibliographic search | |
| Widespread structure library in structure input form | |
| Host organism and NCBI TaxID filters in Taxonomic search | |
| Structure parser and error detector for annotators | |
| Generator of templates for annotators, including NMR-templates | |
| 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 submission, import and export | |
| SOAP API and integration with GLYCOSCIENCES.de | |
| User feedback form | |
| Start of collecting data | |
| Linear structure encoding language | |
| Architectural studies |
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