Databases and associated tools for glycomics and glycoproteomics

Frederique Lisacek, Julien Mariethoz, Davide Alocci, Pauline M. Rudd, Jodie L. Abrahams, Matthew P. Campbell, Nicolle H. Packer, Jonas Ståhle, Göran Widmalm, Elaine Mullen, Barbara Adamczyk, Miguel A. Rojas-Macias, Chunsheng Jin, Niclas G. Karlsson*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

29 Citations (Scopus)

Abstract

The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (Sugar Bind).

Original languageEnglish
Title of host publicationHigh-throughput glycomics and glycoproteomics
Subtitle of host publicationMethods and protocols
EditorsGordan Lauc, Manfred Wuhrer
Place of PublicationNew York
PublisherHumana Press Inc.
Chapter18
Pages235-264
Number of pages30
ISBN (Electronic)9781493964932
ISBN (Print)9781493964918
DOIs
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1503
ISSN (Print)10643745

Keywords

  • Databases
  • Glycobioinformatics
  • HPLC
  • Mass spectrometry
  • NMR
  • Oligosaccharide
  • Omics

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