About GLYCOSCIENCES.de


The GLYCOSCIENCES.de project started in the 1990s with the development of glyco-related databases and tools in the Molecular Modeling Group of Willi von der Lieth at the German Cancer Research Center (DKFZ) in Heidelberg, Germany. The SWEET program and its successor SWEET-II have been the first web-based molecular builders for carbohydrate 3D structures.
In the late 1990s the SweetDB project started to make data from the (at that time discontinued) Complex Carbohydrate Structure Database / CarbBank available over the internet and to link 3D-models of the carbohydrates calculated with Sweet-II to the corresponding entries. Experimental data from NMR experiments were adopted from SugaBase, and later further NMR data were manually extracted from the literature.
Carbohydrates in the Protein Data Bank (PDB) form another data source of glycosciences.de. Several tools are available to access or analyze those data.

After Willi's unexpected death in Nov. 2007 the group was headed by Martin Frank, but the DKFZ had decided to discontinue the project. Therefore, a new home for glycosciences.de had to be found. The server migrated to the University of Gie├čen in March 2010, where it is currently maintained in the group of Thomas Lütteke.


References


Selected references about GLYCOSCIENCES.de:

  • Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth C-W:
    GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research.
    Glycobiology 2006, 16:71R-81R.

  • Loss A, Lütteke T:
    Using NMR data on GLYCOSCIENCES.de.
    Methods Mol Biol 2015, 1273: 87-95

  • Rojas-Macias MA, Lütteke T:
    Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity.
    Methods Mol Biol 2015, 1273: 215-226

  • Emsley P, Brunger AT, Lütteke T:
    Tools to Assist Determination and Validation of Carbohydrate 3D Structure Data.
    Methods Mol Biol 2015, 1273: 229-240

  • Rojas-Macias MA, Loss A, Bohne-Lang A, Frank M, Lütteke T:
    Databases and Tools of GLYCOSCIENCES.de Web Server
    in: Taniguchi N, Endo T, Hart GW, Seeberger PH, Wong CH (Eds), Glycosciences: Biology and Medicine, 2014, Springer, Tokyo, pp. 233-239

  • Kumar S, Lütteke T, Schwartz-Albiez R:
    GlycoCD: a repository for carbohydrate-related CD antigens
    Bioinformatics 2012, 28(19): 2553-2555

  • Frank M, Schloissnig S:
    Bioinformatics and molecular modeling in glycobiology
    Cell Mol Life Sci 2010, 67:2749-2772.

  • Lütteke T, von der Lieth C-W:
    Data mining the PDB for glyco-related data.
    Methods Mol Biol 2009, 534:293-310.

  • Lütteke T
    Analysis and validation of carbohydrate three-dimensional structures.
    Acta Crystallogr D Biol Crystallogr 2009, 65(Pt 2):156-168.

  • Frank M, Lütteke T, von der Lieth C-W:
    GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages.
    Nucleic Acids Res 2007, 35:287-290.

  • Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth C-W:
    Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.
    Nucleic Acids Res 2007, 35:D280-286.

  • Loss A, Stenutz R, Schwarzer E, von der Lieth C-W:
    GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface.
    Nucleic Acids Res 2006, 34:W733-737.

  • Lütteke T, von der Lieth C-W:
    The protein data bank (PDB) as a versatile resource for glycobiology and glycomics.
    Biocatalysis and Biotransformation 2006, 24:147-155.

  • Bohne-Lang A, von der Lieth C-W:
    GlyProt: in silico glycosylation of proteins.
    Nucleic Acids Res 2005, 33:W214-219.

  • Lütteke T, Frank M, von der Lieth C-W:
    Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB.
    Nucleic Acids Res 2005, 33:D242-246.

  • von der Lieth C-W:
    An endorsement to create open access databases for analytical data of complex carbohydrates.
    J Carbohydr Chem 2004, 23:277-297.

  • von der Lieth C-W, Bohne-Lang A, Lohmann KK, Frank M:
    Bioinformatics for glycomics: status, methods, requirements and perspectives.
    Brief Bioinform 2004, 5:164-178.

  • Lütteke T, von der Lieth C-W:
    pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.
    BMC Bioinformatics 2004, 5:69.

  • Lütteke T, Frank M, von der Lieth C-W:
    Data mining the protein data bank: automatic detection and assignment of carbohydrate structures.
    Carbohydr Res 2004, 339:1015-1020.

  • Lohmann KK, von der Lieth C-W:
    GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates.
    Nucleic Acids Res 2004, 32:W261-W266.

  • Frank M, Gutbrod P, Hassayoun C, von der Lieth C-W:
    Dynamic Molecules: molecular dynamics for everyone. An Internet-based access to molecular dynamic simulations: Basic concepts.
    J Mol Model 2003, 9:308-315.

  • Loss a, Bunsmann P, Bohne A, Loss A, Schwarzer E, Lang E, von der Lieth C-W:
    SWEET-DB: an attempt to create annotated data collections for carbohydrates.
    Nucleic Acids Res 2002, 30:405-408.

  • Bohne-Lang A, Lang E, Forster T, von der Lieth C-W:
    LINUCS: linear notation for unique description of carbohydrate sequences.
    Carbohydr Res 2001, 336:1-11.

  • Bohne A, Lang E, von der Lieth C-W:
    SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.
    Bioinformatics 1999, 15:767-768.


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