Database Resources



GlycomeDB

Meta database that integrates the structures from several glycomics databases (CFG, KEGG, GLYCOSCIENCES.de, GlycoBase, JCGGDB, BCSDB, PDB, GlycO and Carbbank) into one consistent sequence representation and creating a unique index of all structures present in the integrated database. Species annotations from the other databases are retrieved as well and integrated using the NCBI Taxonomy. Each structure in GlycomeDB is linked back to the original database allowing finding and browsing all occurrences of a structure in multiple databases.


   
Data in Database structure, databases references, species annotation
Search Options structure search, sub-structure search, similarity search, maximum common substructure search, species search
Availability http://www.glycome-db.org
License None
Status stable, maintained
Funding -
Future Plans -
Code Availablity on request
Contact Rene Ranzinger: rene@ccrc.uga.edu



UniCarbKB

The UniCarb KnowledgeBase (UniCarbKB) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating structural, experimental and functional glycoscience information. This initiative builds upon the success of the glycan structure database GlycoSuiteDB, together with the informatic standards introduced by EUROCarbDB, to provide a high-quality and updated resource to support glycomics and glycoproteomics research. UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information.


   
Data in Database structure, glycoproteins, site-specific information, databases references, species annotation, tissue, cell line, biological fluid, methods
Search Options structure search, sub-structure search, species search, glycoprotein search, UniProtKB accession number search, tissue search, composition search
Availability http://unicarbkb.org
License CC
Status stable, maintained
Funding The National eResearch Collaboration Tools and Resources (NeCTAR) Project; Swiss National Science Foundation
Future Plans Continued curation, better integration and support for GlycoRDF, improved search and query functionality
Code Availablity Release 1 GitHub public, On-going developments BitBucket user managed
Contact -



Carbohydrate Structure Database (CSDB)

The Carbohydrate Structure Databases (CSDBs) store structural, bibliographic, taxonomic, NMR spectroscopic, and other data on natural carbohydrates and their derivatives published in the scientific literature. The CSDB project was launched in 2005 for bacterial saccharides (as BCSDB). Currently, it includes two parts, the Bacterial CSDB and the Plant&Fungal CSDB. In March 2015, these databases were merged to the single Carbohydrate Structure Database (CSDB). The combined CSDB includes information on bacterial and archaeal glycans and derivatives (the coverage is close to complete), as well as on plant and fungal glycans and glycoconjugates (almost all structures published up to 1998). CSDB is regularly updated via manual expert annotation of original publications. Both newly annotated data and data imported from other databases are manually curated. The CSDB data are exportable in a number of modern formats, such as GlycoRDF. CSDB provides additional services for simulation of 1H, 13C and 2D NMR spectra of saccharides, NMR-based structure prediction, glycan-based taxon clustering, and other.


   
Data in Database structures, NMR spectra, taxon annotations, bibliographic annatations, databases references, supplementary data
Search Options structure search, sub-structure search, composition search, taxon search, bibliography search, NMR signal search, id search
Availability http://csdb.glycoscience.ru
License None (free)
Status stable, maintained
Funding Russian Foundation for Basic Research
Future Plans see papers
Code Availablity no
Contact Phyl Toukach: netbox@toukach.ru



SugarBindDB

The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan-binding event is associated with at least one published reference. The core data of SugarBindDB is a triple constituted of a pathogenic agent, a lectin/adhesin and a glycan ligand. SugarBindDB content is displayed in views. All views are interconnected.


   
Data in Database structure, pathogenic lectin/adhesin, protein-carbohydrate interactions, cross-references, binding annotation, tissue, disease, symptoms, methods
Search Options species search, lectin search, ligand search, tissue search, disease search, multi-criteria search
Availability http://sugarbind.expasy.org
License CC
Status stable, maintained
Funding SIB Swiss Institute of Bioinformatics + Swiss National Fund
Future Plans increased data integration, continued data curation, addition of binding prediction tools
Code Availablity https://bitbucket.org/sib-pig/sugarbind
Contact -



Glycosciences.DB

Database of the Glycosciences.de portal. Contains CarbBank structures + PDB carbohydrates + structures with NMR shifts extracted from the literature.


   
Data in Database structure, 3D structure models, pdb data, nmr shifts, species annotation, literature references
Search Options structure search, sub-structure search, motif search, n-glycan properties search, literature search, nmr peak search
Availability http://www.glycosciences.de/database
License None
Status stable, maintained
Funding -
Future Plans -
Code Availablity -
Contact Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de



MonosaccharideDB

Monosaccharide database. Contains monosaccharides + name parsing / encoding routines.


   
Data in Database monosaccharide properties, residue names
Search Options name search, properties search
Availability http://www.mononsaccharidedb.org
License -
Status stable, maintained
Funding -
Future Plans -
Code Availablity -
Contact Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de



GlycoMapsDB

Database of conformational maps of glycosidic linkages


   
Data in Database conformational maps derived from MD simulations
Search Options disaccharide search
Availability http://www.glycosciences.de/modeling/glycomapsdb
License -
Status stable
Funding -
Future Plans -
Code Availablity -
Contact Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de



GlyTouCan

Glycan structure/sequence/composition repository


   
Data in Database Glycan structures, as images, GlycoCT and WURCS, and their motifs, monosaccharides and linked to other related databases including GlycomeDB, BCSDB, GlycoEpitope, with others continuing to be added. Each glycan structure is assigned a GlyTouCan ID.
Search Options Graphical and textual substructure search, ID search and motif search
Availability http://www.glytoucan.org
License CC-BY
Status stable, maintained
Funding Integrated Database Project of Japan
Future Plans Incorporation of UniCarbKB and other JCGGDB databases
Code Availablity open source
Contact Kiyoko F. Aoki-Kinoshita: kkiyoko@soka.ac.jp



GlycoPattern

GlycoPattern is Web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics. This resource includes algorithms and tools to discover structural motifs, a heatmap visualization to compare multiple experiments, hierarchical clustering of Glycan Binding Proteins with respect to their binding motifs and a structural search feature on the experimental data.


   
Data in Database -
Search Options -
Availability https://glycopattern.emory.edu
License -
Status -
Funding -
Future Plans -
Code Availablity -
Contact sanjay.agravat@emory.edu



UniCarb-DB

UniCarb-DB is the glycomics fragmentation database that stores, integrates and processes data from manually annotated ms spectra.


   
Data in Database MS/MS spectra, structures, peak lists, references, methods, tissue and taxonomy annotations
Search Options Species, tissue, composition, recorded mass, observed mass, peak list
Availability http://www.unicarb-db.org
License CC
Status Stable, maintained
Funding NeCTAR, ANDS, STINT, SIB ExPASy
Future Plans -
Code Availablity Open Source
Contact niclas.karlsson@medkem.gu.se



GlycoNAVI

GlycoNAVI is the Carbohydrate database to support carbohydrate research. Contains glycan structures, chemical synthesis, anomeric isomer proportion, NMR spectra, activity, 3D-structures, and carbohydrate-protein interaction extracted from literatures.


   
Data in Database Glycan structures, chemical synthesis, carbohydrate-protein interaction, 3D-structures, and linked to other related databases.
Search Options  
Availability http://glyconavi.org
License CC-BY
Status stable, maintained
Funding Integrated Database Project of Japan, KAKENHI
Future Plans  
Code Availablity  
Contact Issaku Yamada: yamadaissaku@gmail.com