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Bioinformatics for Glycobiology and Glycomics: An by Claus-Wilhelm von der Lieth, Thomas Luetteke, Martin Frank

By Claus-Wilhelm von der Lieth, Thomas Luetteke, Martin Frank

This publication is the 1st to be devoted to the bioinformatics of carbohydrates and glycoproteins.   It presents an creation to this rising box of technological know-how either for the experimentalist operating in glycobiology and glycomics, and likewise for the pc scientist trying to find heritage info for the advance of hugely subtle algorithmic approaches.  The e-book presents an outline of the state of the art within the box, with stories on databases, and the instruments in use for research, interpretation, and prediction of the constructions of complicated carbohydrates, and demonstrates the price of bioinformatics for glycobiology. 

the supply of accomplished databases and corresponding bioinformatics instruments, to entry and examine the massive quantities of experimental information with regards to the constitution of carbohydrates, should be a prerequisite for the good fortune of the large-scale glycomics initiatives that objective to decipher new, thus far unknown, organic services of glycans.   Efficient bioinformatics descriptions and instruments can significantly improve the potency of glycomics learn, when it comes to facts caliber, research and experimental expenses.

for an entire realizing of the molecular techniques during which carbohydrates are concerned, equivalent to protein–carbohydrate interactions and the impression of glycosylation on protein functionality, wisdom of the 3D constitution of the carbohydrate, the protein–carbohydrate advanced, or the glycoprotein is frequently necessary. This e-book offers a radical creation into equipment used for conformational research of carbohydrates.

Key good points:

  • Describes bioinformatic methods to deal with carbohydrate-active enzymes and glycosylation.
  • Provides an outline on bioinformatics instruments that facilitate research of carbohydrate constructions.
  • Gives creation 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 info for Bioinformatics for Glycobiology and Glycomics: An Introduction

Example text

Stevens J, Blixt O, Glaser L, Taubenberger JK, Palese P, Paulson JC, Wilson IA: Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol 2006, 335:1143–1155. 42. Glaser L, Stevens J, Zamarin D, Wilson IA, Garc´ıa-Sastre A, Tumpey TM, Basler CF, Taubenberger JK, Palese P: A single amino acid substitution in 1918 influenza virus hemagglutinin changes receptor binding specificity. J Virol 2005, 79:11533–11536. 43.

Filled columns indicate the cumulative number of glyco-related enzymes reported during the past two decades. Open columns indicate the number of novel enzymes reported in each year. Reprinted from [24] with permission from Elsevier. well-conserved sequence motifs. Based on this knowledge and the increasing availability of gene sequences and the development of appropriate bioinformatics searching algorithms, the in silico identification of GT genes could be successfully applied [21, 22]. 3). This was due to the substantial increase in sequenced genes and the ease of finding new GT genes by homology searching using well-known BLASTN searches.

One of the challenges in glycobiology is the accurate and thorough description and/or representation of the complex structures of carbohydrates, and the sequences of polysaccharides. 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.

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