title: Databases and Associated Tools for Glycomics and Glycoproteomics.
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).
authors.affiliation: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
authors.forename: Frederique
authors.initials: F
authors.lastname: Lisacek
authors.affiliation: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
authors.forename: Julien
authors.initials: J
authors.lastname: Mariethoz
authors.affiliation: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Alocci
authors.affiliation: NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland.
authors.forename: Pauline M
authors.initials: PM
authors.lastname: Rudd
authors.affiliation: Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia.
authors.forename: Jodie L
authors.initials: JL
authors.lastname: Abrahams
authors.affiliation: Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Campbell
authors.affiliation: Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia.
authors.forename: Nicolle H
authors.initials: NH
authors.lastname: Packer
authors.affiliation: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Ståhle
authors.affiliation: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
authors.forename: Göran
authors.initials: G
authors.lastname: Widmalm
authors.affiliation: The MITRE Corporation, McLean, VA, USA.
authors.forename: Elaine
authors.initials: E
authors.lastname: Mullen
authors.affiliation: NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland.|Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
authors.forename: Barbara
authors.initials: B
authors.lastname: Adamczyk
authors.affiliation: Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Rojas-Macias
authors.affiliation: Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
authors.forename: Chunsheng
authors.initials: C
authors.lastname: Jin
authors.affiliation: 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.
authors.forename: Niclas G
authors.initials: NG
authors.lastname: Karlsson
mesh_terms: D000818:Animals; D002236:Carbohydrate Conformation; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D062126:Databases, Chemical; D030562:Databases, Protein; D054794:Glycomics / Q000379:methods*; D006023:Glycoproteins / Q000737:chemistry*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011134:Polysaccharides / Q000737:chemistry*; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D006023:Glycoproteins; D011134:Polysaccharides
keywords: Databases; Glycobioinformatics; HPLC; Mass spectrometry; NMR; Oligosaccharide; Omics