Overview of databases available within the Glycosciences.de web portal
Glycosciences.DB is the main glycan structure database of the Glycosciences.de portal. 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.
The GlycoCD database is a manually curated, comprehensive repository of CD (cluster of differentiation) antigens which are
a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids, or
b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins.
The database is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This database is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner.
Carbohydrates are rather flexible molecules. The shape of a glycan is mainly determined by the torsions of the glycosidic linkages between individual monosaccharides. These torsions are described by phi and psi angles. GlycoMapsDB stores conformational maps of glycans, which describe the conformational space that can be adopted by the glycan.
Carbohydrates are much more complex than other biopolymers such as proteins or nucleic acids. The most often stated reason for this complexity is the fact that their single residues, the monosaccharides, can be linked in several ways, which allows the formation of branched structures. An at least equally important reason for the complexity of carbohydrates, however, is the large number of different monosaccharides, which by far exceeds the number of amino acids (20) or nucleotides (4 DNA + 4 RNA).
MonosaccharideDB is intended to be a comprehensive resource of these monosaccharides. Due to the large number of possible modifications, it is virtually impossible to pre-fill the database with all theoretically conceivable monosaccharide residues. If a requested monosaccharide is not yet in the database, most data can be generated on the fly and displayed to the user (provided the requested residue is a valid monosaccharide).