An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge
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DOI：
10.1093/protein/gzx008
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发表时间：
2017-03-01
影响因子：
2.4
通讯作者：
Martin, M. J.
中科院分区：
文献类型：
--
作者：
Pundir, S.;Onwubiko, J.;Martin, M. J.
酶是生命过程的关键组成部分，对于医学、生物技术、生物加工和药物研究等各个研究领域越来越重要。酶门户网站的目标是为所有欧洲生物信息学研究所（EMBL-EBI）关于酶的数据提供接口（deMatos，P.，例如，（2013），BMC Bioinformatics，14（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）、欧洲蛋白质数据库（PDBe），（Valenkar，S.，例如，Nucleic Acids Res.2016; 44，D385-D395）Rhea-酶催化反应的数据库（Morgat，A.，例如，Nucleic Acids Res.2015; 43，D459-D464），Reactome-生物化学途径数据库（Fabregat，A.，例如，Nucleic Acids Res.2016; 44，D481-D487），IntEnz-a resource with enzyme nomenclature information（Fleischmann，A.，例如，Nucleic Acids Res. 2004 32，D434-D437）和ChEBI（Hastings，J.，例如，Nucleic Acids Res. 2013）和ChEMBL（Bento，A. P.，例如，Nucleic Acids Res. 201442，1083 - 1090）-含有关于小分子化学和生物活性的信息的资源。本文介绍了酶门户网站的重新设计和增加的功能，以最大限度地整合和解释这些数据。酶门户网站的用例示例及其支持的通用工作流程。我们欢迎为一体化提供新资源的建议。
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 (deMatos, P., et al., (2013), BMC Bioinformatics, 14 (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; 44, D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al., Nucleic Acids Res. 2015; 43, D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al., Nucleic Acids Res. 2016; 44, D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al., Nucleic Acids Res. 2004 32, D434-D437) and ChEBI (Hastings, J., et al., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al., Nucleic Acids Res. 201442, 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.