Glycoinformatics

Written in the successful Methods in Molecular Biology series format, the book entitled Glycoinformatics provides current computational methods and protocols used in contemporaneous facets of glycoscience. These are 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. Of particular relevance are the emerging fields addressing the needs of encoding, storing, and analyzing carbohydrate ‘sequences’ and their taxonomy using computers.

• Annotation of Glycomics MS and MS/MS Spectra Using the GlycoWorkbench Software Tool, D. Damerell et al.
• GlycoBase and autoGU : Resources for Interpreting HPLC-Glycan Data, M. Campbell, et al.
• NMR Chemical Shift Prediction of Glycans : Application of the Computer Program CASPER in Structural Analysis, M. Lundborg et al.
• Handling and Conversion of Carbohydrate Sequence Formats and Monosaccharide Notation, T. Lütteke
• Bacterial, Plant, and Fungal Carbohydrate Structure Databases : Daily Usage, P.V. Toukach, et al.
• Using NMR Data on GLYCOSCIENCES.de, A. Loss et al.
• Glycomic Analysis Using KEGG GLYCAN, K.F. Aoki-Kinoshita et al.
• GlycomeDB, R. Ranzinger et al.
• Eukaryotic Glycosylation : Online Methods for Site Prediction on Protein Sequences H.J. Joshi, et al.
• Analyzing Glycan Structure Synthesis with the Glycan Pathway Predictor (GPP) Tool, K.F. Aoki-Kinoshita et al.
• Functional Network in Posttranslational Modifications : Glyco-Net in Glycoconjugate Data Bank, N. Miura et al.
• JCGGDB : Japan Consortium for Glycobiology and Glycotechnology Database
M. Maeda, et al.
• Glycan Array Data Management at Consortium for Functional Glycomics, M. Venkataraman et al.
• Analyzing Glycan-Binding Patterns with the ProfilePSTMM Tool, K.F. Aoki-Kinoshita
• Exploring the Specificities of Glycan-Binding Proteins Using Glycan Array Data and the GlycoSearch Software, D. Kletter et al.
• Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity, M.A. Rojas-Macias et al.
• Tools to Assist Determination and Validation of Carbohydrate 3D Structure Data
P. Emsley et al.
• Glyco3D : A Portal for Structural Glycosciences, S. Pérez et al.
• Solution Conformation of Carbohydrates : A View by Using NMR Assisted by Modeling, D. Díaz et al.
• Informing Saccharide Structural NMR Studies with Density Functional Theory Calculations, T. Klepach et al.
• Energy Maps for Glycosidic Linkage Conformations, A.D French.
• Conformational Analysis of Oligosaccharides and Polysaccharides Using Molecular Dynamics Simulations, M. Frank.
• Molecular Dynamics Simulations of Membrane- and Protein-Bound Glycolipids Using GLYCAM, M.L. DeMarco.
• Lipopolysaccharide Membrane Building and Simulation, S. Jo, Sunhwan et al.
• Molecular Dynamics Simulations of Glycoproteins Using CHARMM, S.S. Mallajosyula et al.