Glycosciences.DB is the main glycan structure database of Glycosciences.de. Each distinct chain, consisting of a carbohydrate part and, if applicable, an aglycon part has a database id, called LinucsID. Additional data, such as bibliographic references, NMR spectra, PDB entries that feature the glycan, etc. are assigned to these entries.
Glycans can be searched by their (sub-)structure, residue composition, N-glycan classification, contained sequence motifs, etc. (see below for a list of all query options). Many query forms allow further restrictions, such as limiting the search to glycans that consist of a certain number of residues, or entries that feature references to PDB entries. That way Glycosciences.DB can be used e.g. to search for specific carbohydrate chains in the PDB, which is not possible at the PDB interfaces so far.
Glycosciences.DB main reference:
Böhm M, Bohne-Lang A, Frank M, Loss A, Rojas-Macias MA, Lütteke TGlycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)
Nucleic Acids Res. 2019, 47(D1):D1195-D1201, doi: 10.1093/nar/gky994
Glycan structure queries:
Glycan composition / classification queries:
Query by experiment
NMR queries:
- Atom search
displays a histogram of all 1H- or 13C-NMR shifts assigned to a certain atom (e.g. H-1 of Galactose) contained in the databank.
- Peak search
compares a list of NMR-shifts (1H- or 13C) given by the user with all spectra contained in the database. A hit-list of spectra and structures in descending order of their spectral similarity is displayed.
- Shift estimation
estimates 1H- or 13C spectra of given structures based on the assumption, that similar structural environments exhibit also similar spectra.
- GlycoNMRSearch
is an external tool that enables a peak search by both 1H and 13C shifts. The results link back to Glycosciences.DB entries.