Keywords:
Proteomics.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (362 pages)
Edition:
1st ed.
ISBN:
9784431564546
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=4760996
DDC:
572.68
Language:
English
Note:
Intro -- Preface -- Contents -- Part I Introduction -- 1 Introduction -- 2 Development of Carbohydrate Nomenclature and Representation -- 2.1 Introduction -- 2.2 Monosaccharides: From Chemical Formula to Structural Formula -- 2.2.1 Chemical Evidence -- 2.2.2 Cyclization of Monosaccharides -- 2.2.3 Naming Monosaccharides and Derivatives -- 2.2.4 Molecular Shapes of Monosaccharides -- 2.2.5 Monosaccharides as Components of Oligosaccharides, Polysaccharides, and Complex Glycans and Glycoconjugates -- 2.3 Representing and Encoding Carbohydrate Structures -- 2.3.1 Representation -- 2.3.2 Graphical Representations -- 2.4 From Graphical Input to Three-Dimensional Structures -- 2.5 In Search of Standards for Representing and Encoding Glycan-Related Information -- 2.6 Databases -- 2.7 Integration -- References -- Part II Monosaccharide and Glycan Structures -- 3 Translation and Validation of Carbohydrate Residue Names with MonosaccharideDB Routines -- 3.1 Introduction -- 3.2 Use Cases -- 3.2.1 Query Options -- 3.2.1.1 Query by Residue Name -- 3.2.1.2 Substituent Query -- 3.2.1.3 Quick Access -- 3.2.2 Residue Name Translation -- 3.2.3 Creating Unique Residue Names -- 3.2.4 MonosaccharideBuilder -- 3.3 Conclusions -- References -- 4 Using GlyTouCan Version 1.0: The First International Glycan Structure Repository -- 4.1 Introduction -- 4.2 Signing In to GlyTouCan -- 4.3 Registration -- 4.3.1 Graphical Interface for Registration -- 4.3.2 Text Input -- 4.3.3 File Upload -- 4.3.4 Registration Results -- 4.4 Search -- 4.4.1 Graphic Input -- 4.4.2 Text Input -- 4.4.3 By Motif -- 4.4.4 By Accession Number -- 4.5 Viewing GlyTouCan Data -- 4.5.1 Glycan Entry -- 4.5.2 Linked Databases -- 4.5.3 Motif List -- 4.5.4 Glycan List -- 4.5.5 User Preferences -- 4.5.6 Graphic Representation -- 4.5.7 Language -- 4.6 Drawing a Glycan Structure by GlycanBuilder.
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4.6.1 File Menu -- 4.6.2 View Menu -- 4.6.3 Structure Menu -- 4.7 Use Cases -- 4.8 Troubleshooting Tips -- References -- 5 Carbohydrate Structure Database (CSDB): Examples of Usage -- 5.1 Introduction -- 5.2 Search Tools -- 5.2.1 Example 1. Study How Introduction of an Amino Group Affects NMR Chemical Shifts of the Lactose Fragment -- 5.2.2 Example 2. Find Bacterial Glycans Containing a Galacturonic Acid Residue and at Least One More Hexose, Published After 2005 in Relation to Antigens -- 5.2.3 Example 3. Find All Compounds Extracted from the Plants of the Genus Solanum Which Contain a Solanidine Constituent -- 5.2.4 Example 4. Find All Carbohydrate Structures Having a Signal Close to 34 ppm in the 13C NMR Spectrum, Except Those Containing Any Octose -- 5.2.5 Example 5. Find All Papers by Knirel or Shashkov AS on Bacterial Structures Containing Quinovose-4-Amine Amidated by Any N-Acetylated Amino Acid -- 5.2.6 Example 6. Find All Bacterial Nonose Monosaccharide Structures (Monomers or Homopolymers) -- 5.3 NMR Tools -- 5.3.1 Example 7. Predict 13C NMR Spectrum of 3-O-α-Abequosyl-6-deoxy-β-d-mannoheptopyranosyl-(d-ribitol-1)-phosphate in Water Solution and Explore Credibility of Chemical Shifts Simulated with Lowest Reported Trustworthiness -- 5.3.2 Example 8. Rank Structural Hypotheses for an Unelucidated Oligomer Conforming to an Experimental 13C NMR Spectrum and Containing Bacillosamine, Galacturonic Acid, and Lysine Residues -- 5.4 Statistical Tools -- 5.4.1 Example 9. Study Monomeric Composition of Two Fungal Species, Aspergillus oryzae and Aspergillus fumigatus, and Reveal Which Monomers Occupy the Termini of Side Chains -- 5.4.2 Example 10. Find Which Dimeric Fragments (Including Sugars, Aglycons, and Other Residues) of Higher Plant Carbohydrates Are Specific to Lupins -- 5.4.3 Example 11. Study Coverage Statistics of Proteobacteria.
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5.5 Conclusion -- References -- Part III Glyco-related Genes and Proteins -- 6 The CAZy Database/the Carbohydrate-Active Enzyme (CAZy) Database: Principles and Usage Guidelines -- 6.1 Classes of CAZy Modules -- 6.2 Browsing the CAZy Website -- 6.2.1 Browsing by CAZy Class and Families -- 6.2.1.1 CAZy Class Webpages -- 6.2.1.2 CAZy Family Webpages -- 6.2.1.3 Recent Addition of Carbohydrate Ligands -- 6.2.2 Browsing by Genome -- 6.3 Retrieving Information from the Search Form/Engine in the CAZy Website -- 6.4 How to Get CAZy to Annotate Your Studied Protein, Genome, or Metagenomic Sample? -- 6.5 What to Do If You Obtain a New Activity or the 3-D Structure for a CAZyme or If You Characterize a New CAZy Family? -- 6.5.1 Novel Activity, 3-D Structure, or New Chemical Information for an Enzyme in an Existing CAZy Family -- 6.5.2 Novel Family in the CAZy Classification -- 6.6 Why Doesn't CAZy Extend Its Classification Scheme to Other Classes of Enzymes? -- 6.7 Why Doesn't CAZy Propagate Experimentally Established Function to Similar Sequences? -- 6.8 Links and Announcements on the CAZy Website -- 6.9 What Is the PULDB Database? -- 6.10 Conclusion -- References -- 7 Glyco3D: A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases -- 7.1 *-8pt -- 7.2 Representing and Encoding Complex Carbohydrates -- 7.3 Glyco3D Portal: An Ensemble of 3D Databases for Glycosciences -- 7.3.1 Monosaccharides -- 7.3.2 Disaccharides -- 7.3.3 BiOligo -- 7.3.4 NMR: A NMR Database of Bioactive Oligosaccharides -- 7.3.5 PolySac: A 3D Structural Database of Polysaccharides -- 7.3.6 GT: A 3D Structural Database of Glycosyltransferases -- 7.3.7 mABS: A 3D Structural Database of Monoclonal Antibodies Against Carbohydrates -- 7.3.8 GAG: 3D Structural Database of Glycosaminoglycan-Binding Proteins.
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7.3.9 LECTIN3D: A 3D Structural Database of Lectins -- 7.4 Sequence Search in the Whole Glyco-3D Portal -- 7.5 Conclusions -- References -- 8 GlycoGene Database (GGDB) on the Semantic Web -- 8.1 System Overview -- 8.2 User Interface -- 8.2.1 Top Page -- 8.2.2 Detail View -- 8.2.2.1 Detail View Overview -- 8.2.2.2 Overview, General Information -- 8.2.2.3 Orthologous Genes -- 8.2.2.4 Acceptor Substrates -- 8.2.2.5 Expression Information -- 8.2.2.6 Human Glycogene GatewayTM Entry Clone Information -- 8.3 Using GGDB Entries as Stanzas -- 8.4 Summary -- References -- 9 KEGG GLYCAN -- 9.1 KEGG Databases -- 9.1.1 KEGG Identifiers -- 9.1.2 KEGG Pathway Maps -- 9.1.3 Glycan Structure Maps -- 9.1.4 KEGG Modules -- 9.1.5 BRITE Hierarchies and Tables -- 9.1.6 KOs, GENES, and GENOME -- 9.1.7 Chemical Compounds, Glycans, and Reactions -- 9.1.8 Diseases and Drugs -- 9.2 KEGG and GenomeNet Tools -- 9.2.1 BlastKOALA -- 9.2.2 KEGG Mapper -- 9.2.3 Ortholog Table and Module Table -- 9.2.4 SSDB and BLAST -- 9.2.5 SIMCOMP and KCaM -- 9.3 KEGG GLYCAN Resource -- 9.3.1 Glycan-Specific Datasets -- 9.3.2 Linking Genes to Glycan Structures -- 9.3.3 Linking Glycans to Diseases -- References -- Part IV Glycoproteomics Data -- 10 Exploring the UniCarbKB Database -- 10.1 Introduction -- 10.1.1 What You Can Currently Find in UniCarbKB -- 10.1.2 Content-Driven Design -- 10.2 Browsing UniCarbKB -- 10.2.1 The UniCarbKB Front Page -- 10.2.2 Finding Taxonomic, Tissue and Glycoprotein Content -- 10.2.2.1 Taxonomy -- 10.2.2.2 Tissue -- 10.2.2.3 Protein and Protein Accession -- 10.2.2.4 Why Is the Autocomplete Useful? -- 10.2.3 Searching by Composition -- 10.2.4 GlycanBuilder and Searching for (Sub)Structures -- 10.2.4.1 Query by Structure -- 10.2.4.2 Glycan Structure Summary Page -- 10.2.4.3 Switching Between Symbol Nomenclatures -- 10.2.5 Exploring and Finding Curated References.
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10.2.5.1 Viewing Individual Publications -- 10.2.5.2 More About the `Biological Associations' -- 10.2.5.3 Inference and Confidence `Validation Methods' -- 10.2.6 Using the Glycoprotein Navigation Page to Find Global and Site-Specific Content -- 10.2.6.1 Viewing Glycoprotein Information -- 10.2.7 Information Available for Taxonomy and Tissue Searches -- 10.2.7.1 More About the Sidebar -- 10.2.7.2 `Connections' - What You Can Find Through UniCarbKB -- 10.3 Summary -- References -- 11 GlycoProtDB: A Database of Glycoproteins Mapped with Actual Glycosylation Sites Identified by Mass Spectrometry -- 11.1 Introduction -- 11.2 The Contents of GlycoProtDB -- 11.3 The Method to Collect Data on the Actual Glycosylation Sites -- 11.4 Construction of Data Resource from MS-Based Identification List of Glycopeptides -- 11.5 How to Use the Database, GlycoProtDB -- 11.6 Search -- 11.7 Search Results -- 11.8 Glycosylation Sites -- 11.9 Links to Other Databases -- 11.10 Download of Whole Data Resources -- References -- Part V Glycan Interactions -- 12 GlycoEpitope -- 12.1 Introduction -- 12.2 Features of GlycoEpitope -- 12.3 Web Interface -- 12.4 Search Tool -- 12.5 How to Operate the GlycoEpitope Database -- 12.5.1 To Find an Epitope Record from "List Epitopes" -- 12.5.2 To Find an Antibody Record from "List Antibodies" -- 12.5.3 Using Search Functions -- 12.5.3.1 Epitope Search Rules -- 12.5.3.2 Antibody Search Rules -- 12.5.3.3 Example of How to Search -- References -- 13 SugarBindDB -- 13.1 Introduction -- 13.2 Case Study 1 -- 13.2.1 Browsing Versus Querying the Database for Pathogens -- 13.2.1.1 Browsing -- 13.2.1.2 Searching -- 13.3 Case Study 2 -- 13.3.1 Search for a Pathogen, Visualise Related Structures and Explore Associations -- 13.4 Case Study 3 -- 13.4.1 Query with Multiple Criteria and Explore Associations -- 13.5 Case Study 4.
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13.5.1 Query with Multiple Pathogen Names, Visualise and Explore Binding Specificity.
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