title: Introduction to informatics in glycoprotein analysis.
abstract: Although the field of glycome informatics has established several methods, standards and technologies for carbohydrate analysis, the analysis of glycoproteins and other glycoconjugates is still in its infancy. However, from even before the term "glycome informatics" emerged, several groups have developed methods and tools on the analysis of glycosylation sites. In particular, the Expasy server has provided such tools to aid in the prediction of glycosylation sites of N- and O-glycans, while glycosciences.de has provided tools for the analysis of the amino acid distribution around glycosylation sites in 3D space, based on data from the Protein Data Bank (PDB). In addition to these tools, databases of glycoprotein information are available that may aid in glycoprotein prediction; GlycoProtDB is a database of glycoprotein information characterized by the Japanese Consortium for Glycobiology and Glycotechnology, and UniProt includes glycosylation site information along with its protein sequence data. Furthermore, the providers of the glycosylation tools on Expasy, the Center for Biological Sequence Analysis, also provide a database of O-glycosylation called O-GlycBase. Such databases may eventually aid in the development of glycoprotein-analysis tools as more consistent data is accumulated, and some prospects on this area of research will be given.
authors.affiliation: Department of Bioinformatics, Soka University, Aliso Viejo, CA, USA. kkiyoko@soka.ac.jp
authors.forename: Kiyoko F
authors.initials: KF
authors.lastname: Aoki-Kinoshita
mesh_terms: D000117:Acetylglucosamine / Q000378:metabolism; D000818:Animals; D030562:Databases, Protein; D054794:Glycomics / Q000379:methods*; D006023:Glycoproteins / Q000032:analysis* / Q000737:chemistry; D006031:Glycosylation; D006801:Humans; D040901:Proteomics / Q000379:methods*
chemical_list: D006023:Glycoproteins; D000117:Acetylglucosamine