S Pundir, J Onwubiko, R Zaru, S Rosanoff, R Antunes, M Bingley, X Watkins, C O'Donovan, M J Martin
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The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al ., Nucleic Acids Res. 2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016; , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res. 2004 , D434-D437) and ChEBI (Hastings, J., et al ., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res. 2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. 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引用次数: 0
摘要
14:酶是生命过程的关键组成部分,在医学、生物技术、生物加工和药物研究等各个研究领域日益重要。酶门户网站的目标是为欧洲生物信息学研究所(EMBL-EBI)关于酶的所有数据提供一个接口(de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103)。这些数据包括酶的功能、序列特征和家族分类、蛋白质结构、反应、途径、小分子、疾病和相关文献。酶数据的来源包括:UniProt 知识库(UniProtKB)(UniProt Consortium,2015 年)、欧洲蛋白质数据库(PDBe)、(Valenkar,S、et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-酶催化反应数据库(Morgat, A., et al ., Nucleic Acids Res. 2015; , D459-D464)、Reactome-生化途径数据库(Fabregat, A.、et al ., Nucleic Acids Res. 2016; , D481-D487)、IntEnz--酶命名信息资源(Fleischmann, A., et al ., Nucleic Acids Res. 2004 , D434-D437)和 ChEBI(Hastings, J.、等人,核酸研究,2013 年)和 ChEMBL(Bento, A. P., et al .本文介绍了对 Enzyme Portal 的重新设计以及为最大限度地整合和解释这些数据而增加的功能。文章还举例说明了酶门户网站及其支持的多功能工作流程。我们欢迎大家提出整合新资源的建议。
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.
14: Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al ., Nucleic Acids Res. 2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016; , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res. 2004 , D434-D437) and ChEBI (Hastings, J., et al ., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res. 2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration.