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Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

ABSTRACT: In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

SUBMITTER: Kleywegt GJ

PROVIDER: S-EPMC10705588 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

Kleywegt Gerard J GJ Adams Paul D PD Butcher Sarah J SJ Lawson Catherine L CL Rohou Alexis A Rosenthal Peter B PB Subramaniam Sriram S Topf Maya M Abbott Sanja S Baldwin Philip R PR Berrisford John M JM Bricogne Gérard G Choudhary Preeti P Croll Tristan I TI Danev Radostin R Ganesan Sai J SJ Grant Timothy T Gutmanas Aleksandras A Henderson Richard R Heymann J Bernard JB Huiskonen Juha T JT Istrate Andrei A Kato Takayuki T Lander Gabriel C GC Lok Shee-Mei SM Ludtke Steven J SJ Murshudov Garib N GN Pye Ryan R Pintilie Grigore D GD Richardson Jane S JS Sachse Carsten C Salih Osman O Scheres Sjors H W SHW Schroeder Gunnar F GF Sorzano Carlos Oscar S COS Stagg Scott M SM Wang Zhe Z Warshamanage Rangana R Westbrook John D JD Winn Martyn D MD Young Jasmine Y JY Burley Stephen K SK Hoch Jeffrey C JC Kurisu Genji G Morris Kyle K Patwardhan Ardan A Velankar Sameer S

ArXiv 20240202

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-d ...[more]

PMID: 38076521

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Project description: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.

Dataset Information

Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

Publications

Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

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