Bioinformatics for Glycobiology and Glycomics (eBook)

Dr. Claus-Wilhelm von der Lieth, died 2007. Thomas Lütteke, Justus-Liebig University Giessen, Germany; Fakulty of Veterinary Medicine, Institute of Biochemistry und Endocrinology. Dr. Martin Frank, German Cancer Research Center, Heidelberg, Germany; Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands.

List of Contributors.

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.

"This is an excellent and timely first comprehensive overview of
the recent efforts directed toward organization and mining of data
produced by the rapidly growing fields of glycobiology and
glycomics." (The Quarterly Review of Biology, 1 March 2011)