Glyco-related Databases and Development of Bioinformatic tools for Glycobiology and Glycomics
 

The human genome seems to encode for not more than 30,000 to 40,000 proteins. A major challenge is to understand how posttranslational events, such as glycosylation, affect the activities and functions of these proteins in health and disease. The importance of protein glycosylation is becoming widely realized through studies on protein folding, protein localization and trafficking, protein solubility, biological half-life as well as studies on cell-cell interactions. The progressing Glycomics projects will dramatically accelerate the understanding of the roles of carbohydrates in cell communication and lead to novel therapeutic approaches for treatment of human disease. The MIT's magazine of innovation (January 21 2003) has identified Glycomics as one of the top ten technologies that will change the future.

To support the upcoming Glycomics projects we focus our research activities on the development of bioinformatic tools and databases for glycobiology.

 
Data Base
 
Short Description
 
Support
   SWEET-DB is our main glycosciences data base which allows glycoscientists to find important data for the compound of interest in a compact and well-structured representation. Currently, reference data taken from CarbBank, which is linked to the NCBI PubMed service, NMR data taken from SugaBase , theoretically calculated MS-spectra and 3D coordinates generated with SWEET-II can be retrieved for a given carbohydrate (sub)structure.
Contact: Willi von der Lieth, Alexander Loss, Klaus Lohmann, Andreas Bohne-Lang, Thomas Lütteke
 
   Glyco-MS-Search DB contains theoretically calculated MS-spectra of all structures contained in SWEET-DB. Glyco-MS-Serach finds all spectra and structures which map with a given list of MS-peaks. A direct link to SWEET-DB entries is established.
Contact: Klaus Lohmann, Willi von der Lieth
 
   GlycoMaps DB is a data base system for the management of conformational maps and profiles, The system allows conformational maps to be archived in a standard format, and it will provide search and comparison facilities. An interface to structures from Sweet-DB is implemented. We also offer scientists the possibility of adding their own publicized structures to the database via a web interface.
Contact: Martin Frank, Willi von der Lieth
 
   PDB2LINUCS automatically extracts carbohydrate information from PDB-files and displays it using the LINUCS-Code. Many PDB-files contain carbohydrate structures. An efficient option to retrieve carbohydrate related information is provided.
Contact: Thomas Lütteke, Willi von der Lieth
 

 
Application
 
Short Description
 
Support
   SWEET-II rapidly converts the primary sequence of a complex carbohydrate, as defined by standard nomenclature, directly into a reliable 3D molecular model by linking together preconstructed 3D molecular templates of monosaccharides in the manner specified by the sequence and then optimizing the 3D structure using the MM3 force field.
Contact: Andreas Bohne, Willi von der Lieth
 
   Glyco-Protein performs an in silico glycosylation of proteins. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II.
Contact: Andreas Bohne, Willi von der Lieth
 
   Glyco-Fragment generates and displays the theoretical fragments of oligosaccharides which occur in MS-spectra. The commonly used extended nomenclature for is used to input the glycan structure.
Contact: Klaus Lohmann, Willi von der Lieth
 
   LiGraph generates schematic drawings of oligosaccharides which are often used to display glycan structure.
Contact: Andreas Bohne, Willi von der Lieth
 
 
'Dynamic Molecules'
 The 'Dynamic Molecules' approach is the first Internet portal which provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The 'expert Mode' allows to explore the conformational space of oligosaccharides.
Contact: Martin Frank, Willi von der Lieth
 

 We have joined the US 'Consortium for Functional Glycomics'. The central aim this program is to 'define paradigms by which protein-carbohydrate interactions mediate cell communication'. Among other approaches this goal shall be archived through the development and maintenance of glycomics databases of human carbohydrate binding proteins, glycosyltransferase genes, and mammalian carbohydrate structures. Based on our ideas how to virtually link distributed data collections, we are involved in discussions how to organize this new infrastructure.

 The Web services that we currently can offer are well accepted by the scientific community . During the last three years, we have had more than 8 Million visits to our Web sitemfrom all parts of the world. More than 40.000 3D structures of oligosaccharides have been constructed with SWEET-II.

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