Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)

Abstract

Glycosciences.DB, the glycan structure database of the Glycosciences.de portal, collects various kinds of data on glycan structures, including carbohydrate moieties from worldwide Protein Data Bank (wwPDB) structures. This way it forms a bridge between glycomics and proteomics resources. A major update of this database combines a redesigned web interface with a series of new functions. These include separate entry pages not only for glycan structures but also for literature references and wwPDB entries, improved substructure search options, a newly available keyword search covering all types of entries in one query, and new types of information that is added to glycan structures. These new features are described in detail in this article, and options how users can provide information to the database are discussed as well. Glycosciences.DB is available at http://www.glycosciences.de/database/ and can be freely accessed.

Figure 1.

Screenshots of Glycosciences.DB glycan structure entry (front, truncated at the dashed line), literature entry (middle) and wwPDB entry (back). All three entries are linked to each other: The wwPDB entry contains both the displayed N-glycan core structure entry and the literature reference. No glycan structure is registered yet with the literature entry; the link to the N-glycan core structure entry is assigned via the wwPDB entry.

Figure 2.

Residue highlighting in a plant N-glycan with core fucosylation and xylose (LinucsID 13934). Without highlighting, the residues are difficult to identify (top). This becomes easier when halos (bottom left) or bond colors (bottom right) are used with colors matching those of the SNFG symbols, even when the structure is oriented in a different way than the SNFG symbols.

Figure 3.

The content summary that is provided with each entry in glycan structure lists offers an overview of the data that are available for that entry. The entry on the top contains a 3D structure model, references to 5 wwPDB entries, 113 literature entries and 2 GlycoMaps, and 10 taxonomy items. The entry in the middle contains a 3D structure model, one 13C NMR spectrum and 3 literature references, and the bottom entry contains 1 literature reference but no further data.

Figure 4.

GlycanBuilder is used to create (sub-)structure search queries graphically (top). The results contain textual and SNFG representations of glycans next to each other (bottom). Whereas the symbols are easy to read for many glycoscientists, the text can be read without knowledge of the symbols. Furthermore, the text offers a highlighting of the substructure that matches the query, and it gives information on aglycones, which are not included in the symbols.