Glycoinformatics

            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