Glycobiology Advance Access originally published online on October 20, 2005
Glycobiology 2006 16(5):71R-81R; doi:10.1093/glycob/cwj049
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GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research
2 Present address: Division of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
3 Present address: Mannheim Medical Research Center, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, D-68135 Mannheim, Germany
4 Present address: Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
Spectroscopic Department (B090), German Cancer Research Center, Molecular Modelling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
1 To whom correspondence should be addressed; w.vonderlieth{at}dkfz.de
Received on August 25, 2005; revised on October 7, 2005; accepted on October 11, 2005
The development of glycan-related databases and bioinformatics applications is considerably lagging behind compared with the wealth of available data and software tools in genomics and proteomics. Because the encoding of glycan structures is more complex, most of the bioinformatics approaches cannot be applied to glycan structures. No standard procedures exist where glycan structures found in various species, organs, tissues or cells can be routinely deposited. In this article the concepts of the GLYCOSCIENCES.de portal are described. It is demonstrated how an efficient structure-based cross-linking of various glycan-related data originating from different resources can be accomplished using a single user interface. The structure oriented retrieval options—exact structure, substructure, motif, composition and sugar components—are discussed. The types of available data—references, composition, spatial structures, nuclear magnetic resonance (NMR) shifts (experimental and estimated), theoretically calculated fragments and Protein Database (PDB) entries—are exemplified for Man3. The free availability and unrestricted use of glycan-related data is an absolute prerequisite to efficiently share distributed resources. Additionally, there is an urgent need to agree to a generally accepted exchange format as well as to a common software interface. An open access repository for glyco-related experimental data will secure that the loss of primary data will be considerably reduced.
Key words: databases/glycobioinformatics/glycomics/structure retrieval
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