Computational tools for Glycomics Studies

Sugars are involved in almost every aspect of biology, from recognising pathogens and to blood clotting.The glycome's basic building blocks are far more numerous and varied than the four letters of the DNA alphabet or the score of amino acids that make proteins.In the late 1980s, when researchers isolated the first gene for a glycosyl transferase, an enzyme that adds sugars to fats and proteins. The discovery gave scientists the first opportunity to study this process, which is usually called glycoslyation, by manipulating the activity of such enzymes.


Fig: Carbohydrate only (no protein) - PDB id:2HYA


Glycomics, or glycobiology is a discipline of biology that deals with the structure and function of oligosaccharides (chains of sugars). The identity of the entirety of carbohydrates in an organism is thus collectively referred to as the glycome.The progressing glycomics projects will dramatically accelerate the understanding of the roles of carbohydrates in cell communication and hopefully lead to novel therapeutic approaches for treatment of human disease

The Functional Glycomics Gateway is a comprehensive and free online resource that is the result of a collaboration between the Consortium for Functional Glycomics (CFG) and Nature Publishing Group. It is aimed at keeping you abreast of developments in the emerging field of functional glycomics.

http://www.functionalglycomics.org/static/index.shtml

For annotation and/or cross-reference carbohydrate-related data collections which will allow us to find important data for compounds of interest in a compact and well-structured representation

http://www.glycosciences.de/sweetdb/

Many pdb-files contain carbohydrate structures. Since there is not such a standard nomenclature like it exists for amino acids, it is difficult to find the carbohydrate information. Sometimes entire oligosaccharides are encoded in one single residue. Information about carbohydrate linkages is often missing, and if it is present, it is not in a unique format and therefore also difficult to find.pdb2linucs automatically extracts carbohydrate information from pdb-files .

http://www.dkfz-heidelberg.de/spec/pdb2linucs/


GlycoSuite comprises GlycoSuiteDB, the leading curated and annotated glycan database, and new bioinformatic tools which interface mass spectrometric data with the database.

https://glycosuite.proteomesystems.com/glycosuite/glycodb

A Complex Carbohydrate Structure Database, also known as CarbBank is available . But, due to lack of funding it is no longer updated.

http://www.boc.chem.uu.nl/sugabase/carbbank.html


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