Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update).

Michael Böhm,Thomas Lütteke,Alexander Loss,Andreas Bohne-Lang,Martin Frank,Miguel A Rojas-Macias

doi:10.1093/nar/gky994

Abstract

Glycosciences.DB, the glycan structure database of the Glycosciences.de portal, collects various kinds of data on glycan structures, including carbohydrate moieties from worldwide Protein Data Bank (wwPDB) structures. This way it forms a bridge between glycomics and proteomics resources. A major update of this database combines a redesigned web interface with a series of new functions. These include separate entry pages not only for glycan structures but also for literature references and wwPDB entries, improved substructure search options, a newly available keyword search covering all types of entries in one query, and new types of information that is added to glycan structures. These new features are described in detail in this article, and options how users can provide information to the database are discussed as well. Glycosciences.DB is available at http://www.glycosciences.de/database/ and can be freely accessed.

Highlights

Carbohydrates, often referred to as glycans, are one of the four major classes of biomolecules, next to nucleic acids, proteins and lipids
A major update of this database combines a redesigned web interface with a series of new functions. These include separate entry pages for glycan structures and for literature references and worldwide Protein Data Bank (wwPDB) entries, improved substructure search options, a newly available keyword search covering all types of entries in one query, and new types of information that is added to glycan structures
We offer the structure in LInear Notation for Unique description of Carbohydrate Sequences (LINUCS) notation [17], the notation internally used in the database to store and identify the glycan structures, and, where possible, in GlycoCT condensed and GlycoCT xml format [18]

Summary

INTRODUCTION

Carbohydrates, often referred to as glycans, are one of the four major classes of biomolecules, next to nucleic acids, proteins and lipids. Carbohydrates are the most abundant and the most complex molecules [1] Besides their well-known functions as energy storage or structural components they are parts of glycoproteins or glycolipids and cover cell surfaces in the glycocalyx [2,3]. They serve as recognition sites for cell–cell and cell–matrix interactions and for pathogens such as viruses, which frequently interact with glycans on the cell surface to enter their host cells.

Entry handling

Content summaries in glycan structure lists

Substructure search algorithm

NMR spectra search

CONCLUSION AND OUTLOOK