Databases and Associated Tools for Glycomics and Glycoproteomics

Methods Mol Biol. 2017;1503:235-264. doi: 10.1007/978-1-4939-6493-2_18.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carbohydrate Conformation
  • Chromatography, High Pressure Liquid / methods
  • Databases, Chemical
  • Databases, Protein
  • Glycomics / methods*
  • Glycoproteins / chemistry*
  • Humans
  • Mass Spectrometry / methods
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Polysaccharides / chemistry*
  • Protein Conformation
  • Proteomics / methods*
  • Software

Substances

  • Glycoproteins
  • Polysaccharides