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Methods Mol Biol. 2017;1503:235-264.

Databases and Associated Tools for Glycomics and Glycoproteomics.

Author information

1
Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
2
NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland.
3
Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia.
4
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
5
The MITRE Corporation, McLean, VA, USA.
6
Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
7
Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden. niclas.karlsson@medkem.gu.se.

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 (SugarBind).

KEYWORDS:

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

PMID:
27743371
DOI:
10.1007/978-1-4939-6493-2_18
[Indexed for MEDLINE]

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