European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
Acta Crystallogr D Struct Biol. 2022 May 1;78(Pt 5):542-552. doi: 10.1107/S205979832200328X. Epub 2022 Apr 20.
The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for the validation of cryo-EM structures, focusing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested metrics as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as nonspecialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. The details of the new resource are described, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to obtain a better understanding of the quality and of the best ways to assess the quality of cryo-EM structures in EMDB and PDB.
电子显微镜数据银行 (EMDB) 是电子低温显微镜 (cryo-EM) 领域的中央档案库，用于存储和传播体积映射和断层扫描图。在社区的参与下，EMDB 开发了新的资源来验证 cryo-EM 结构，重点关注体积数据的质量以及任何模型的拟合质量，这些模型本身都存档在蛋白质数据银行 (PDB) 中。基于社区专家的建议，验证资源是在三级系统中开发的。第 1 层涵盖了广泛而不断发展的验证指标集，包括经过验证的指标和更实验性的指标，这些指标是为所有 EMDB 条目计算的，并在验证分析 (VA) 网络资源中呈现。这个系统对于 cryo-EM 专家特别有用，既可以验证单个结构，也可以评估新验证指标的实用性。第 2 层包含 VA 资源中涵盖的验证指标的子集，这些指标经过了广泛的测试，被认为对专家和非专家都有用。这些指标在 EMDB 网站上整个档案的条目特定网页上呈现。随着在 VA 资源中包含的指标方面获得更多经验，预计社区将就适合纳入第 2 层系统的指标子集达成共识。最后，第 3 层由全球蛋白质数据银行 (wwPDB) 联盟产生的验证报告和服务器组成。来自第 2 层的成功指标将被提议纳入 wwPDB 验证管道和报告中。新资源的详细信息被描述，重点是第 1 层系统。所有这三个层次的输出都是公开的，要么通过 EMDB 网站（第 1 层和第 2 层），要么通过 wwPDB ftp 站点（第 3 层），尽管所有三个层次的内容都会随着时间的推移而演变（第 1 层最快，第 3 层最慢）。我们希望这些验证资源将帮助 cryo-EM 社区更好地了解 EMDB 和 PDB 中 cryo-EM 结构的质量和评估质量的最佳方法。
