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.

Bioinformatics for Glycobiologyand Glycomics 3
Contents 7
List of Contributors 11
Preface 17
Section 1: Introduction 25
1. Glycobiology, Glycomics and (Bio)Informatics 27
Section 2: Carbohydrate Structures 45
2. Introduction to Carbohydrate Structure and Diversity 47
3. Digital Representations of Oligo- and Polysaccharides 73
4. Evolutionary Considerations in Studying the Sialome: Sialic 93
Section 3: Carbohydrate-active Enzymes and Glycosylation 113
5. Carbohydrate-active Enzymes Database: Principles and Classification of Glycosyltransferases 115
6. Other Databases Providing Glycoenzyme Data 143
7. Bioinformatics Analysis of Glycan Structures from a Genomic Perspective 149
8. Glycosylation of Proteins 167
9. Prediction of Glycosylation Sites in Proteins 187
Section 4: Experimental Methods – Bioinformatic Requirements 217
10. Experimental Methods for the Analysis of Glycans and Their Bioinformatics Requirements 219
11. Analysis of N- and O-Glycans of Glycoproteins by HPLC Technology 227
12. Glycomic Mass Spectrometric Analysis and Data Interpretation Tools 247
13. Software Tools for Semi-automatic Interpretation of Mass Spectra of Glycans 281
14. Informatics Concepts to Decode Structure-Function Relationships of Glycosaminoglycans 293
15. NMR Databases and Tools for Automatic Interpretation of Spectra of Carbohydrates 319
16. Automatic Spectrum Interpretation Based on Increment Rules: CASPER 335
17. Interpretation of 13C NMR Spectra by Artificial Neural Network Techniques (NeuroCarb) 345
Section 5: 3D Structures of Complex Carbohydrates 359
18. Conformational Analysis of Carbohydrates – A Historical Overview 361
19. Predicting Carbohydrate 3D Structures Using Theoretical Methods 383
20. Synergy of Computational and Experimental Methods in Carbohydrate 3D Structure Determination and Validation 413
Section 6: Protein–Carbohydrate Interaction 437
21. Structural Features of Lectins and Their Binding Sites 439
22. Statistical Analysis of Protein–Carbohydrate Complexes Contained in the PDB 457
Section 7: Appendices 471
Appendix 1: List of Available Websites 473
Appendix 2: Glossary 477
Index 485
Color Plates 497
Cover Page 505

"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)