Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive.
The inaugural symposium will be held May 4-5, 2021 in an event hosted by the American Society for Biochemistry and Molecular Biology and organized by the wwPDB Foundation.
This celebration of the 50th anniversary of the founding of the Protein Data Bank as the first open access digital data resource in biology will include presentations from speakers from around the world who have made tremendous advances in structural biology and bioinformatics.
Attendees are encouraged to participate in the virtual poster session and exhibition hall. Students and postdoctoral fellows will be eligible for poster awards.
Register and submit abstracts by March 15th, 2021 for reduced rates.
Speakers will include:
The online sessions will take place between 11 a.m. – 4:30 p.m. EST each day. The event will be recorded and made available to registered participants after the meeting.
Sponsorship opportunities are available; please contact the wwPDB Foundation for more information.
The wwPDB archive has now been updated to include validation reports for every released set of EM model coordinates in the PDB and every released EMDB map entry. Validation reports provide quantitative and visual assessments of structure quality and enable archive-wide comparisons (https://www.wwpdb.org/validation/validation-reports).
wwPDB EM validation reports were first made available to OneDep depositors in 2019 (http://www.wwpdb.org/news/news?year=2019#5db841ceea7d0653b99c8839). The current reports are based on recommendations obtained from EM Validation Task Force (VTF) meetings in 2010 (Structure 20: 205-214, wwpdb.org/task/em) and 2020 (white paper in preparation), as well as EM Validation Challenge events (https://www.ncbi.nlm.nih.gov/pubmed/32002441, https://www.biorxiv.org/content/10.1101/2020.06.12.147033v1). Examples of recent improvements include images for deposited masks, improved map-model overlay images, visualization of a (approximate) raw map from two half-maps, and rotationally averaged power spectrum plots. The underlying methodology is continually improved, based on community requirements, requests and feedback.
The PDB Core Archive holds validation reports that assess each PDB model along with its associated experimental map/tomogram from EMDB. EM map+model reports can be downloaded at the following wwPDB mirrors:
The EMDB Core Archive holds validation reports that assess each EMDB map/tomogram entry. EM map-only reports can be downloaded at the following URLs:
Additional information about validation reports is available for EM map+model, EM map only, and EM tomograms.
If you have any questions or queries about wwPDB validation, please contact us at email@example.com.
A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 5th, 2021 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.
The directory 20210105 includes the structure and experimental data for the 173,005 PDB entries available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core archive is 822 GB.
A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 4, 2021 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20210101/ and ftp://snapshots.pdbj.org/20210101/. The snapshot of EMDB Core archive contains map files and their metadata within XML files for both released and obsoleted entries (13731 and 142, respectively) and is 2.9 TB in size.