Glycoinformatics
(Sprache: Englisch)
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...
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Klappentext zu „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.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.
Inhaltsverzeichnis zu „Glycoinformatics “
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
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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 TvaroSka
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Autoren-Porträt
Martin Frank, geboren 1950, lebt in Zürich. Er hat zahlreiche Romane und Erzählungen veröffentlicht.
Bibliographische Angaben
- 2015, 2015, XVI, 506 Seiten, 146 farbige Abbildungen, Masse: 18,3 x 26 cm, Gebunden, Englisch
- Herausgegeben: Thomas Lütteke, Martin Frank
- Verlag: Springer, Berlin
- ISBN-10: 1493923420
- ISBN-13: 9781493923427
- Erscheinungsdatum: 10.03.2015
Sprache:
Englisch
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