Glycoinformatics

Kiyoko F. Aoki-Kinoshita; Matthew P. Campbell; Frederique Lisacek; Sriram Neelamegham; William S. York; Nicolle H. Packer

doi:10.1101/glycobiology.4e.52

Glycoinformatics

Review

In: Essentials of Glycobiology [Internet]. 4th edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2022. Chapter 52.

Authors

Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, Frederique Lisacek, Sriram Neelamegham, William S. York, Nicolle H. Packer

Book Editors

Book Affiliations

¹ Distinguished Professor of Medicine and of Cellular & Molecular Medicine, Co-Director, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California, USA
² Professor of Surgery, Beth Israel Deaconess Medical Center, Director, National Center for Functional Glycomics, Harvard Medical School, Boston, Massachusetts, USA
³ Distinguished Professor of Cellular & Molecular Medicine, Co-Director, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California, USA
⁴ Horace W. Goldsmith Foundation Chair, Professor of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
⁵ Sr. Eminent Scholar in Drug Discovery, Georgia Research Alliance William Henry Terry Professor of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
⁶ Professor of Mycology, ETH Zürich, Institute of Microbiology, Department of Biology, Zürich, Switzerland
⁷ Distinguished Research Professor, Georgia Athletics Association Professor in Complex Carbohydrate Research, Professor of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
⁸ Endowed Chair and Professor, Yabumoto Department of Intractable Disease Research, Research Institute for Microbial Diseases, Immunology Frontier Research Center, Osaka University, Osaka, Japan
⁹ Distinguished Professor of Molecular Sciences, Macquarie University, Sydney, Australia and Principal Research Leader, Institute for Glycomics, Griffith University, Gold Coast, Australia
¹⁰ Professor and Eminent Scholar Emeritus, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
¹¹ Professor, Departments of Pharmacology and Neuroscience, Johns Hopkins University, Baltimore, Maryland, USA
¹² Director of Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany, Professor, Freie Universität, Berlin, Germany

PMID: 35536985
Bookshelf ID: NBK579995
DOI: 10.1101/glycobiology.4e.52

Excerpt

Glycans are branched, biosynthetic metabolic products that are commonly encoded by multiple genes. Unique genes may be involved in the biosynthesis of specific glycan classes (glycoprotein, glycolipid, glycosaminoglycans etc.), and at the same time, many glycogenes participate in the biosynthesis of more than one glycan class. These intricacies relating to gene expression, enzyme specificity, endoplasmic reticulum (ER)–Golgi compartment–specific localization of enzymes, the branched nature of glycan structures, and species-specific variation in monosaccharide composition makes the analysis of glycosylation processes complicated. To aid this effort, a variety of analytical methods have been developed to identify and quantify the structure of glycans and their conjugates in biological samples. Glycoinformatics tools and software aim to use computers to integrate these experimental data, using our knowledge of glycan biosynthetic pathways as a backbone. Glycoinformatics databases ideally curate experimental data allowing glycan structures to be rigorously defined, archived, organized, searched, and annotated. When linked to other relational databases, glycoscience data may then be integrated with related genomic, transcriptomic, proteomic, lipidomic, and metabolomic information. This chapter describes the current status of glycoinformatics databases and software development, with focus on efforts to bridge the gap between glycan structure and function.

Sections

Publication types

Review