Bioinformatics for Glycobiology and Glycomics: An Introduction

Preface (Claus-Wilhelm von der Lieth).

Section 1: Introduction.

1. Glycobiology, Glycomics and (Bio)Informatics (Claus-Wilhelm von der Lieth).

Section 2: Carbohydrate Structures.

2. Introduction to Carbohydrate Structure and Diversity (Stephan Herget, René Ranzinger, Robin Thomson, Martin Frank and Claus-Wilhelm von der Lieth).

3. Digital Representations of Oligo- and Polysaccharides (Stephan Herget and Claus-Wilhelm von der Lieth).

4. Evolutionary Considerations in Studying the Sialome: Sialic Acids and the Host–Pathogen Interface (Amanda L. Lewis and Ajit Varki).

Section 3: Carbohydrate-active Enzymes and Glycosylation.

5. Carbohydrate-active Enzymes Database: Principles and Classification of Glycosyltransferases (Pedro M. Coutinho, Corinne Rancurel, Mark Stam, Thomas Bernard, Francisco M. Couto, Etienne G. J. Danchin and Bernard Henrissat).

6. Other Databases Providing Glycoenzyme Data (Thomas L¨utteke and Claus-Wilhelm von der Lieth).

7. Bioinformatics Analysis of Glycan Structures from a Genomic Perspective (Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa).

8. Glycosylation of Proteins (Claus-Wilhelm von der Lieth and Thomas Lüteke).

9. Prediction of Glycosylation Sites in Proteins (Karin Julenius, Morten B. Johansen, Yu Zhang, Søren Brunak and Ramneek Gupta).

Section 4: Experimental Methods – Bioinformatic Requirements.

10. Experimental Methods for the Analysis of Glycans and Their Bioinformatics Requirements (Claus-Wilhelm von der Lieth).

11. Analysis of N- and O-Glycans of Glycoproteins by HPLC Technology (Anthony H. Merry and Sviatlana A. Astrautsova).

12. Glycomic Mass Spectrometric Analysis and Data Interpretation Tools (Niclas G. Karlsson and Nicolle H. Packer).

13. Software Tools for Semi-automatic Interpretation of Mass Spectra of Glycans (Kai Maass and Alessio Ceroni).

14. Informatics Concepts to Decode Structure-Function Relationships of Glycosaminoglycans (Rahul Raman, S. Raguram and Ram Sasisekharan).

15. NMR Databases and Tools for Automatic Interpretation of Spectra of Carbohydrates (Claus-Wilhelm 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 and Beat Ernst).

Section 5: 3D Structures of Complex Carbohydrates.

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 and Martin Frank).

Section 6: Protein–Carbohydrate Interaction.

21. Structural Features of Lectins and Their Binding Sites (Remy Loris).

22. Statistical Analysis of Protein–Carbohydrate Complexes Contained in the PDB (Thomas Lütteke and Claus-Wilhelm von der Lieth).

Section 7: Appendices.

Appendix 1: List of Available Websites.

Appendix 2: Glossary.

Index.