By Claus-Wilhelm von der Lieth, Thomas Luetteke, Martin Frank
This ebook is the 1st to be devoted to the bioinformatics of carbohydrates and glycoproteins. It offers an creation to this rising box of technology either for the experimentalist operating in glycobiology and glycomics, and likewise for the pc scientist trying to find history info for the advance of hugely refined algorithmic approaches. The e-book offers an summary of the cutting-edge within the box, with studies on databases, and the instruments in use for research, interpretation, and prediction of the buildings of advanced carbohydrates, and demonstrates the worth of bioinformatics for glycobiology.
the provision of complete databases and corresponding bioinformatics instruments, to entry and examine the big quantities of experimental facts with regards to the constitution of carbohydrates, can be a prerequisite for the luck of the large-scale glycomics initiatives that objective to decipher new, thus far unknown, organic capabilities of glycans. Efficient bioinformatics descriptions and instruments can significantly increase the potency of glycomics learn, by way of information caliber, research and experimental bills.
for an entire realizing of the molecular techniques during which carbohydrates are concerned, reminiscent of protein–carbohydrate interactions and the effect of glycosylation on protein functionality, wisdom of the 3D constitution of the carbohydrate, the protein–carbohydrate complicated, or the glycoprotein is frequently necessary. This booklet offers an intensive advent into equipment used for conformational research of carbohydrates.
Key positive aspects:
- Describes bioinformatic techniques to address carbohydrate-active enzymes and glycosylation.
- Provides an outline on bioinformatics instruments that facilitate research of carbohydrate buildings.
- Gives advent into molecular modelling of carbohydrate 3D constitution and carbohydrates inside the Protein Databank.
- Assumes just a easy wisdom of biology and bioinformatics.
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Additional resources for Bioinformatics for Glycobiology and Glycomics: An Introduction
1 Carbohydrates in Drug and Vaccine Development Bacteria, viruses, and parasites are the major agents leading to disease. All cells in nature are covered with a dense and complex coat of glycans. A wide variety of pathogens initiate infection by binding to the surface glycans of host cells. This is not surprising as cell-surface glycans are the first molecules encountered by pathogens when they contact potential host cells or their secretions. Outer, terminal glycan sequences such as those carrying sialic acid residues are even more likely to be preferred targets, as they are the first residues that pathogens encounter.
The aglycones may be proteins, lipids or small molecules. Abstractly speaking, the glycosidic bond can be seen as an analog to the commonly known peptide bond of proteins or phosphodiester bonds in nucleic acids. The basic monosaccharides may lose chirality at certain C-atoms through deoxygenation (OH group replaced by H), a phenomenon frequently observed in natural monosaccharides. Other typical modifications are introduction of acidic functions, double bond formation, shifts of the carbonyl function or the attachment of small chemical groups (substituents).
G. g. 1). From a glycoinformatics point of view, different encoding schemes for monosaccharides are in use, many of which have some limitations (see Chapter 3). org) to harmonize carbohydrate sequences in globally distributed carbohydrate structure databases. As a result, GlycomeDB can collate information from the seven major open-access databases. The following sections provide an overview of the structural diversity of carbohydrate sequences1 derived from this data source. This chapter presents an overview of carbohydrate nomenclature and structure definitions, and provides an insight into the theoretical and actual diversity of carbohydrate structures.