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.
Daftar Isi
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 (Neuro Carb) (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.
Tentang Penulis
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.
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