Glycoinformatics

This book provides current glycoinformatics methods and protocols used to support the determination of carbohydrate structures in biological samples as well as carbohydrate structure databases, the interaction of carbohydrates with proteins, and theoretical and experimental methods to study their three-dimensional structure and dynamics. Glycoinformatics explores this recently emerged field, which has come into being in order to address the needs of encoding, storing, and analyzing carbohydrate ‘sequences’ and their taxonomy using computers. Written in the highly successful Methods in Molecular Biology series format, chapters contain the kind of detailed description and key implementation advice to ensure successful results.

Part I: Software Tools for Experimental Glycan Analysis and Profiling

1. Annotation of Glycomics MS and MS/MS Spectra Using the GlycoWorkbench Software Tool

            David Damerell, Alessio Ceroni, Kai Maass, Rene Ranzinger, Anne Dell, and Stuart M. Haslam

2. GlycoBase and autoGU: Resources for Interpreting HPLC-Glycan Data

            Matthew P. Campbell, Lousie Royle, and Pauline M. Rudd

3. NMR Chemical Shift Prediction of Glycans: Application of the Computer Program CASPER in Structural Analysis

            Magnus Lundborg and Göran Widmalm

Part II: Glycosylation: Storing and Managing Carbohydrate Structure Data

4. Handling and Conversion of Carbohydrate Sequence Formats and Monosaccharide Notation

            Thomas Lütteke

5. Bacterial, Plant, and Fungal Carbohydrate Structure Databases: Daily Usage

            Philip V. Toukach and Ksenia S. Egorova

6. Using NMR Data on GLYCOSCIENCES.de

            Alexander Loss and Thomas Lütteke

7. Glycomic Analysis Using KEGG GLYCAN

            Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa

8. GlycomeDB

            René Ranzinger and William S. York

Part III: “Understanding” Glycosylation

9. Eukaryotic Glycosylation: Online Methods for Site-Prediction on Protein Sequences

            Hiren J. Joshi and Ramneek Gupta

10. Analyzing Glycan Structure Synthesis with the Glycan Pathway Predictor (GPP) Tool

            Kiyoko F. Aoki-Kinoshita

11. Functional Network in Post-Translational Modifications: Glyco-Net in Glycoconjugate Data Bank

            Nobuaki Miura, Takuya Okada, Daisuke Murayama, Kazuko Hirose, Taku Sato, Ryo Hashimoto, and Nobuhiro Fukushima

Part IV: Protein-Carbohydrate Interaction: Databases

12. JCGGDB: Japan Consortium for Glycobiology and Glycotechnology DataBase

            Masako Maeda, Noriaki Fujita, Yoshinori Suzuki, Hiromichi Sawaki, Toshihide Shikanai, and Hisashi Narimatsu

13. Glycan Array Data Management at Consortium for Functional Glycomics

            Maha Venkataraman, Ram Sasisekharan, and Rahul Raman

Part V: Protein-Carbohydrate Interaction: Data Mining

14. Analyzing Glycan Binding Patterns with the ProfilePSTMM Tool

            Kiyoko F. Aoki-Kinoshita

15. Exploring the Specificities of Glycan-Binding Proteins Using Glycan Array Data and the GlycoSearch Software

            Doron Kletter, Bryan Curnutte, Kevin Maupin, Marshall Bern, and Brian B. Haab

16. Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity

            Miguel A. Rojas-Macias and Thomas Lütteke

Part VI: Structural Glycoinformatics: Databases and Tools  

17. Tools to Assist Determination and Validation of Carbohydrate 3D Structure Data

            Paul Emsley, Axel T. Brunger, and Thomas Lütteke

18. Glyco3D : A Portal for Structural Glycosciences

            Serge Pérez, Anita Sarkar, Alain Rivet, Christelle Breton, and Anne Imberty

Part VII: Structural Glycoinformatics: Structure Determination and Simulation

19. Solution Conformation of Carbohydrates: A View by Using NMR Assisted by Modeling

            Dolores Díaz, Angeles Canales-Mayordomo, F. Javier Cañada, and Jesús Jiménez-Barbero

20. Informing Saccharide Structural NMR Studies with Density Functional

Theory Calculations

            Thomas Klepach, Hongqiu Zhao, Xiaosong Hu, Wenhui Zhang, Roland Stenutz, Matthew J. Hadad, Ian Carmichael, and Anthony S. Serianni

21. Energy Maps for Glycosidic Linkage Conformations

            Alfred D. French

22. Conformational Analysis of Oligo- and Polysaccharides Using Molecular Dynamics Simulations

            Martin Frank

23. Molecular Dynamics Simulations of Membrane- and Protein-Bound Glycolipids Using GLYCAM

            Mari L. DeMarco

24. Lipopolysaccharide Membrane Building and Simulation

            Sunhwan Jo, Emilia L. Wu, Danielle Stuhlsatz, Jeffery B. Klauda, Alexander D. MacKerell, Jr., Göran Widmalm, and Wonpil Im

25. Molecular Dynamics Simulations of Glycoproteins Using CHARMM

            Sairam S. Mallajosyula, Sunhwan Jo, Wonpil Im, and Alexander D. MacKerell, Jr.

26. Calculating Binding Free Energies for Protein-Carbohydrate Complexes

            Jodi A. Hadden, Matthew B. Tessier, Elisa Fadda, and Robert J. Woods

27. Scoring Functions for AutoDock

            Anthony D. Hill and Peter J. Reilly

28. Structures of Glycans Bound to Receptors from Saturation Transfer Difference (STD) NMR Spectroscopy: Quantitative Analysis by Using CORCEMA-ST

            Pedro M. Enríquez-Navas, Cinzia Guzzi, Juan C. Muñoz-García, Pedro M. Nieto, and Jesús Angulo

29. QM/MM Methods for Studying Enzymatic Reactions of Glycosyltransferases

            Igor Tvaroška