Glycoinformatics

TRAMA

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.

SOMMARIO

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 FunctionalTheory 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

ALTRE INFORMAZIONI

• Condizione: Nuovo
• ISBN: 9781493923427
• Collana: Methods in Molecular Biology
• Dimensioni: 254 x 178 mm Ø 12375 gr
• Formato: Copertina rigida
• Illustration Notes: XVI, 506 p. 182 illus., 146 illus. in color.
• Pagine Arabe: 506
• Pagine Romane: xvi