Glycoinformatics
Author(s)
Bibliographic Information
Glycoinformatics
（Methods in molecular biology / John M. Walker, series editor, 1273）（Springer protocols）
Humana Press, c2015
- : pbk
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Note
"Softcover reprint of the hardcover 1st edition 2015."--T.p. verso
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Authoritative and timely, Glycoinformatics demonstrates the progress that has been achieved in glycoinformatics, which indicates that it is no longer a niche subject covered by only a few scientists but is truly coming of age.
Table of Contents
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 Goeran Widmalm
Part II: Glycosylation: Storing and Managing Carbohydrate Structure Data
4. Handling and Conversion of Carbohydrate Sequence Formats and Monosaccharide Notation
Thomas Lutteke
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 Lutteke
7. Glycomic Analysis Using KEGG GLYCAN
Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa
8. GlycomeDB
Rene 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 Lutteke
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 Lutteke
18. Glyco3D : A Portal for Structural Glycosciences
Serge Perez, 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 Diaz, Angeles Canales-Mayordomo, F. Javier Canada, and Jesus Jimenez-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., Goeran 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. Enriquez-Navas, Cinzia Guzzi, Juan C. Munoz-Garcia, Pedro M. Nieto, and Jesus Angulo
29. QM/MM Methods for Studying Enzymatic Reactions of Glycosyltransferases
Igor Tvaroska
by "Nielsen BookData"
