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Bioinformatics for Glycobiology and Glycomics: An Introduction


Description: This book is the first to be dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides an introduction to this emerging field of science both for the experimentalist working in glycobiology and glycomics, and also for the computer scientist looking for background information for the development of highly sophisticated algorithmic approaches. The book provides an overview of the state-of-the-art in the field, with reviews on databases, and the tools in use for analysis, interpretation, and prediction of the structures of complex carbohydrates, and demonstrates the value of bioinformatics for glycobiology.

The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs.

For a complete understanding of the molecular processes in which carbohydrates are involved, such as protein–carbohydrate interactions and the impact of glycosylation on protein function, knowledge of the 3D structure of the carbohydrate, the protein–carbohydrate complex, or the glycoprotein is often indispensable. This book provides a thorough introduction into methods used for conformational analysis of carbohydrates.

Key features:
- Describes bioinformatic approaches to handle carbohydrate-active enzymes and glycosylation.
- Provides an overview on bioinformatics tools that facilitate analysis of carbohydrate structures.
- Gives introduction into molecular modelling of carbohydrate 3D structure and carbohydrates contained in the Protein Databank.
- Assumes only a basic knowledge of biology and bioinformatics.

Recent advances in sequence determination for complex carbohydrates should lead to the generation of large amounts of data relating to their sequence and structure. Interpretation of this sequence information will require new bioinformatics tools.  Several groups worldwide are defining the basic principles of how best to encode and store the structures of complex carbohydrates. The  automated interpretation of experimental data, especially mass spectra, is currently the most active area of research. The availability of comprehensive databases and corresponding bioinformatics tools to access and analyse the data will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. This book is the first dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides a state of the art overview and demonstrates the value of bioinformatics for glycobiology, not simply as a review of databases and tools but rather as an introduction to a new branch of glycobiology. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. The objective of the book is to illustrate ways to use bioinformatics to enhance glycomics data mining and improve glycomics analysis.


Contents: Preface

1. Glycobiology, Glycomics and (Bio)Informatics – Claus-Wilhelm von der Lieth
2. Introduction to Carbohydrate Structure and Diversity – Stephan Herget, René Ranzinger, Robin Thomson, Martin Frank, Claus-W. von der Lieth
3. Digital Representations of oligo-and polysaccharides – Stephan Herget, Claus-W. von der Lieth
4. Evolutionary Considerations in Studying the Sialome: Sialic Acids and the Host–Pathogen Interface – Amanda L. Lewis and Ajit Varki
5. Carbohydrate-active Enzymes Database: Principles and Classification of Glyosyltransferases – Pedro M. Coutinho, Corinne Rancurel, Mark Stam, Thomas Bernard, Francisco M. Couto, Etienne G. J. Danchin, Bernard Henrissat
6. Other Databases Providing Glycoenzyme Data – Thomas Lütteke, Claus-W. von der Lieth
7. Bioinformatics Analysis of Glycan Structures from a Genomic Perspective – Kiyoko F. Aoki-Kinoshita
8. Glycosylation of Proteins – Claus-W. von der Lieth and Thomas Lütteke
9. Prediction of Glycosylation Sites in Proteins – Karin Julenius, Morten B. Johansen, Yu Zhang, Søren Brunak, Ramneek Gupta
10. Experimental Methods for the Analysis of Glycans and their Bioinformatics Requirements – Claus-W. von der Lieth
11. Analysis of N- and O-glycans of Glycoproteins by HPLC Technology – Anthony H. Merry, Sviatlana A. Astrautsova
12. Glycomic Mass Spectrometric Analysis and Data Interpretation Tools – Niclas G. Karlsson, Nicolle H. Packer
13. Software Tools for Semi-Automatic Interpretation of Mass Spectra of Glycans – Kai Maass, Alessio Ceroni
14. Informatics Concepts to Decode Structure-Function Relationships of Glycosaminoglycans – Rahul Raman, S. Raguram, Ram Sasisekharan
15. NMR Databases and Tools for Automatic Interpretation of Spectra of Carbohydrates – Claus-W. von der Lieth
16. Automatic Spectrum Interpretation Based on Increment Rules: CASPER – Roland Stenutz
17. Interpretation of 13C-NMR Spectra by Artificial Neural Network Techniques (NeuroCarb) – Andreas Stoeckli, Matthias Studer, Brian Cutting, Beat Ernst
18. Conformational Analysis of Carbohydrates – A Historical Overview – Martin Frank
19. Predicting Carbohydrate 3D Structures Using Theoretical Methods – Martin Frank
20. Synergy of Computational and Experimental Methods in Carbohydrate 3D Structure Determination and Validation – Thomas Lütteke, Martin Frank
21. Structural Features of Lectins and Their Binding Sites – Remy Loris
22. Statistical Analysis of Protein Carbohydrate Complexes Contained in the PDB – Thomas Lütteke, Claus-W. von der Lieth

Appendix A. List of Available Websites

Appendix B. Glossary




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