Sanja Abbott, Andrii Iudin, Paul K. Korir, Sriram Somasundharam, Ardan Patwardhan
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{"title":"EMDB Web Resources","authors":"Sanja Abbott, Andrii Iudin, Paul K. Korir, Sriram Somasundharam, Ardan Patwardhan","doi":"10.1002/cpbi.48","DOIUrl":null,"url":null,"abstract":"<p>The Electron Microscopy Data Bank (EMDB) is a global, openly accessible archive of biomolecular and cellular 3-D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops Web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualizing EMDB structures, statistically analyzing EMDB content, and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive, and a form-based search. For visualization, the ‘volume slicer’ enables slices of EMDB entries to be visualized interactively and in three orthogonal directions. The <i>EMstats</i> Web service provides up-to-date interactive statistical charts analyzing EMDB. All EMDB entries have ‘Visual Analysis’ pages that provide basic validation information for the entry. © 2018 by John Wiley & Sons, Inc.</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"61 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2018-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.48","citationCount":"15","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current protocols in bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpbi.48","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 15
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Abstract
The Electron Microscopy Data Bank (EMDB) is a global, openly accessible archive of biomolecular and cellular 3-D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops Web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualizing EMDB structures, statistically analyzing EMDB content, and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive, and a form-based search. For visualization, the ‘volume slicer’ enables slices of EMDB entries to be visualized interactively and in three orthogonal directions. The EMstats Web service provides up-to-date interactive statistical charts analyzing EMDB. All EMDB entries have ‘Visual Analysis’ pages that provide basic validation information for the entry. © 2018 by John Wiley & Sons, Inc.
EMDB网页资源
电子显微镜数据库(EMDB)是一个全球性的，开放访问的生物分子和细胞三维重建档案，来源于电子显微镜(EM)数据。EMBL-EBI开发基于web的资源，以促进EMDB数据的重用。在这里，我们提供了如何使用这些资源来搜索EMDB、可视化EMDB结构、统计分析EMDB内容和检查EMDB结构的有效性的协议。搜索协议包括来自主页的快速链接类别、指向每周周期中发布的最新条目的链接、对整个存档的过滤浏览以及基于表单的搜索。对于可视化，“音量切片器”使EMDB条目的切片能够在三个正交的方向上交互式地可视化。EMstats Web服务提供最新的交互式统计图表来分析EMDB。所有EMDB条目都有“可视化分析”页面，为条目提供基本的验证信息。©2018 by John Wiley &儿子,Inc。
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