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Protein Data Bank to Absorb 3D Biological Maps Database


The Electron Microscopy Data Bank, a database that contains three-dimensional maps of biological specimens and associated data from electron microscopy experiments, will become part of the Protein Data Bank archive on March 7.

According to the PDB, database users will see a change in the download links for the maps once the two resources have merged. However, researchers will still be able to deposit maps and models via the EMDataBank website.

Furthermore, all 3D EM map depositions will continue to receive EMDB IDs and all coordinate entries will continue to receive PDB IDs, the group said.

Additional information about the merger, as well as detailed specifications for data access, is available here.

The merger is part of the PDB's goal to maintain a freely available public archive of macromolecular structural data from all structure determination methods as well as its efforts to develop a Common Deposition & Annotation Tool that covers all experimental methods including hybrids, PDB partner organizations said in a statement.

Currently, PDB has more than 77,000 coordinate entries, nearly all with associated experimental data, including 57,000 X-ray entries with structure factor files and 6,400 NMR entries with restraints.

The combined resources will include more than 1,200 electron microscopy-derived biological maps that are currently available in EMDB with coordinates for 400 EM map-derived models in PDB.

With the added EMDB data, the size of the PDB archive will increase from 130 gigabytes to roughly 180 gigabytes. Sites that mirror the full archive will need to increase their storage capacity accordingly, the group said.

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