2024-07-17 : 37051 EMDB map entries, 21507 PDB coordinate entries RCSB PDB | PDBe

EMDB Policies and Procedures Document Now Available

To ensure consistent and coherent rules for EMDB data processing, a comprehensive policy and procedures document has been drawn up for the EMDB and is now available to view on the EMDB website.

Founded in 2002, the Electron Microscopy Data Bank (EMDB) was created as a public archive for three-dimensional (3D) electron cryo-microscopy (cryo-EM) maps and tomograms of biomacromolecules, their complexes and cellular structures. In 2002, the first eight EMDB entries were released. Since then, EMDB releases have steadily increased with the number of entries released so far in 2019 (2,401) being more than double the number released in 2017 (1,108). To help deal with the cryo-EM data deluge, EMDB has drawn up guidelines and policies to facilitate EM data deposition and release through the wwPDB OneDep system.

Some highlights of the policy document include EMDB’s recommendation for single-particle depositions to include a primary map (as shown in the accompanying publication), a raw map (unmasked, unfiltered, unsharpened) and unmasked half-maps, as well as any auxiliary files such as Fourier Shell Correlation (FSC) data. EMDB also advises that the official wwPDB validation report generated after biocuration, which now includes EM map/tomogram validation and, if applicable, map-model validation, is provided to journal editors and referees as part of the manuscript submission and review process. Furthermore, details on data requirements, accepted formats, entry modifications and the release process are provided.

Recently, there has been increasing demand within the cryo-EM community to make all data publicly available. It is for this reason EMDB strongly encourages the deposition of all atomic models to the Protein Data Bank (PDB), all 3D EM reconstructions to EMDB and all raw data (including tilt series for tomograms) to the Electron Microscopy Public Image Archive (EMPIAR). Related entries in these archives reference one another, making your data easily findable and accessible to the community.

As EMDB approaches the milestone of 10,000 entries, EMDB’s policies and processing procedures should help support and guide users through the process from data deposition to structure release.

Source: wwPDB News

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