糖组学和糖蛋白质组学的数据库及相关工具

Databases and Associated Tools for Glycomics and Glycoproteomics.

作者信息

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

机构信息

Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland.

出版信息

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

DOI:10.1007/978-1-4939-6493-2_18

PMID:27743371

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).

摘要

事实证明，访问用于糖组学和糖蛋白质组学的生物数据库对于当前的糖生物学研究至关重要。本章介绍了致力于糖生物信息学不同方面的现有数据库。这包括寡糖序列数据库、实验数据库、（聚糖和糖相关蛋白的）三维结构数据库以及聚糖与组织、疾病和蛋白质的关联。还提供了使用与实验数据库相关的工具将原始糖分析数据转换为聚糖结构信息的特定搜索协议。特别是，使用U/HPLC（GlycoBase）、MS（GlycoWorkbench、UniCarb-DB、GlycoDigest）和NMR（CASPER）进行糖分析方法的研究人员将从本章中受益。此外，我们还包括有关如何利用聚糖结构信息查询将聚糖与蛋白质相关联（UniCarbKB）以及与病原体相互作用（SugarBind）的数据库的信息。