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Glycoinformatics

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Cover of 'Glycoinformatics'

Table of Contents

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    Book Overview
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    Chapter 1 Annotation of Glycomics MS and MS/MS Spectra Using the GlycoWorkbench Software Tool.
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    Chapter 2 GlycoBase and autoGU: Resources for Interpreting HPLC-Glycan Data.
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    Chapter 3 NMR Chemical Shift Prediction of Glycans: Application of the Computer Program CASPER in Structural Analysis.
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    Chapter 4 Handling and conversion of carbohydrate sequence formats and monosaccharide notation.
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    Chapter 5 Bacterial, plant, and fungal carbohydrate structure databases: daily usage.
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    Chapter 6 Using NMR Data on GLYCOSCIENCES.de.
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    Chapter 7 Glycomic Analysis Using KEGG GLYCAN.
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    Chapter 8 GlycomeDB.
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    Chapter 9 Eukaryotic glycosylation: online methods for site prediction on protein sequences.
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    Chapter 10 Analyzing Glycan Structure Synthesis with the Glycan Pathway Predictor (GPP) Tool.
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    Chapter 11 Functional network in posttranslational modifications: glyco-net in glycoconjugate data bank.
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    Chapter 12 JCGGDB: Japan Consortium for Glycobiology and Glycotechnology Database.
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    Chapter 13 Glycan array data management at consortium for functional glycomics.
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    Chapter 14 Analyzing Glycan-Binding Patterns with the ProfilePSTMM Tool.
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    Chapter 15 Exploring the Specificities of Glycan-Binding Proteins Using Glycan Array Data and the GlycoSearch Software.
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    Chapter 16 Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity.
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    Chapter 17 Tools to Assist Determination and Validation of Carbohydrate 3D Structure Data.
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    Chapter 18 Glyco3D: A Portal for Structural Glycosciences.
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    Chapter 19 Solution conformation of carbohydrates: a view by using NMR assisted by modeling.
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    Chapter 20 Informing saccharide structural NMR studies with density functional theory calculations.
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    Chapter 21 Energy maps for glycosidic linkage conformations.
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    Chapter 22 Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.
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    Chapter 23 Molecular Dynamics Simulations of Membrane- and Protein-Bound Glycolipids Using GLYCAM.
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    Chapter 24 Lipopolysaccharide membrane building and simulation.
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    Chapter 25 Molecular Dynamics Simulations of Glycoproteins Using CHARMM.
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    Chapter 26 Calculating binding free energies for protein-carbohydrate complexes.
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    Chapter 27 Scoring Functions for AutoDock.
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    Chapter 28 Structures of Glycans Bound to Receptors from Saturation Transfer Difference (STD) NMR Spectroscopy: Quantitative Analysis by using CORCEMA-ST
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    Chapter 29 QM/MM Methods for Studying Enzymatic Reactions of Glycosyltransferases.
Attention for Chapter 11: Functional network in posttranslational modifications: glyco-net in glycoconjugate data bank.
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Chapter title
Functional network in posttranslational modifications: glyco-net in glycoconjugate data bank.
Chapter number 11
Book title
Glycoinformatics
Published in
Methods in molecular biology, February 2015
DOI 10.1007/978-1-4939-2343-4_11
Pubmed ID
Book ISBNs
978-1-4939-2342-7, 978-1-4939-2343-4
Authors

Nobuaki Miura, Takuya Okada, Daisuke Murayama, Kazuko Hirose, Taku Sato, Ryo Hashimoto, Nobuhiro Fukushima, Miura, Nobuaki, Okada, Takuya, Murayama, Daisuke, Hirose, Kazuko, Sato, Taku, Hashimoto, Ryo, Fukushima, Nobuhiro

Editors

Thomas Lütteke, Martin Frank

Abstract

Elucidating pathways related to posttranslational modifications (PTMs) such as glycosylation is of growing importance in post-genome science and technology. Graphical networks describing the relationships among glycan-related molecules, including genes, proteins, lipids, and various biological events, are considered extremely valuable and convenient tools for the systematic investigation of PTMs. Glyco-Net ( http://bibi.sci.hokudai.ac.jp/functions/ ) can dynamically make network figures among various biological molecules and biological events. A certain molecule or event is expressed with a node, and the relationship between the molecule and the event is indicated by arrows in the network figures. In this chapter, we mention the features and current status of the Glyco-Net and a simple example of the search with the Glyco-Net.

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Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 March 2015.
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#20,264,045
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