GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages.
Conformational energy maps of the glycosidic linkages are a valuable resource to gain information about preferred conformations and flexibility of carbohydrates. Here we present GlycoMapsDB, a new database containing more than 2500 calculated conformational maps for a variety of di- to pentasaccharide fragments contained in N- and O-glycans. Oligosaccharides representing branchpoints of N-glycans are included in the set of fragments, thus the influence of neighbouring residues is reflected in the conformational maps. During refinement of new crystal structures, maps contained in GlycoMapsDB can serve as a valuable resource to check whether the torsion values of a glycosidic linkage are located in an 'allowed' region similar to the Ramachandran plot analysis for proteins. This might help to improve the structural quality of the glycan data contained in the Protein Data Bank (PDB). A link between GlycoMapsDB and the PDB has been established so that the glycosidic torsions of all glycans contained in the PDB can be retrieved and compared to calculated data. The service is available at www.glycosciences.de/modeling/glycomapsdb/.
Frank
M
M
German Cancer Research Center, Spectroscopic Department (B090) Molecular Modeling Group, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. m.frank@dkfz.de
Lütteke
T
T
von der Lieth
C-W
CW
D002236:Carbohydrate Conformation; D016208:Databases, Factual; D020407:Internet; D009844:Oligosaccharides / Q000737:chemistry*; D011134:Polysaccharides / Q000737:chemistry; D014584:User-Computer Interface
D009844:Oligosaccharides; D011134:Polysaccharides