Nucleic Acids Research, 2007, Vol. 35, No. suppl_1 287-290
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages
German Cancer Research Center, Spectroscopic Department (B090) Molecular Modeling Group, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany 1 Bijvoet Center for Biomolecular Research, Department of Bioorganic Chemistry, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands
*To whom correspondence should be addressed. Tel: +49 6221 424541; Fax: +49 6221 42454; Email: m.frank{at}dkfz.de
Received August 16, 2006. Revised October 11, 2006. Accepted October 12, 2006.
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/.
Present address:
T. Lütteke, Massachusetts Institute of Technology, Biological Engineering, 77 Massachusetts Avenue, 16-719 Cambridge, MA 0213, USA
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