Data Deposition/Biocuration Services and
Archive Management

In 2022, 16,344 experimentally-determined structures were deposited to the archive. Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

Of all structures deposited this year, 85.1% were deposited with a release status of hold until publication; 7.5% were released as soon as annotation of the entry was complete; and 7.4% were held until a particular date. 65.1% of these entries were determined by X-ray crystallographic methods; 1.8% were determined by NMR methods; and 33% by 3DEM.

6,004 EMDB maps were released in the archive.

14,292 new PDB structures were released in 2022 They account for 7.2% of the year-end total holdings of 199,803 available entries. 1,151 SARS-CoV-2 structures were released, for a total of 2,868 available at the start of the new year.

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web browsers (Chrome and Firefox) have dropped support for the FTP protocol, which has effectively discontinued the FTP protocol for non-technical users.

Given that the majority of file download activity on the internet has moved to HTTP/S, wwPDB plans to deprecate FTP download protocol on November 1, 2024.

wwPDB has traditionally supported FTP, together with HTTP/S and RSYNC. Gradual deprecation of the FTP protocol, in favor of the HTTP/HTTPS protocol will be approached while maintaining support for the RSYNC protocol which offers additional functionality compared to the other 2 protocols.

As announced previously, DNS names specific to the protocols have been introduced:

  1. for HTTP/S
  2. for FTP. To be deprecated on November 1st 2024. Note that from September 2023 this DNS name will not accept HTTP/S traffic.
  3. for RSYNC

Starting September 2023, wwPDB will start enforcing use of these updated DNS names for the preparation of FTP protocol deprecation.

Please contact with any questions.

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wwPDB operations are governed by the wwPDB Charter (PDF), which was most recently renewed in 2021. The renewed agreement provides for two types of wwPDB membership--Full and Associate.

Current wwPDB Full Members include three founding members [Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, USA), Protein Data Bank in Europe (PDBe, United Kingdom), and Protein Data Bank Japan (PDBj, Japan)] and two specialist data resource members [Biological Magnetic Resonance Bank (BMRB, USA and Japan; joined in 2006) and Electron Microscopy Data Bank (EMDB, United Kingdom; joined in 2021)].

Full Members jointly manage three wwPDB Core Archives, including the Protein Data Bank, the Biological Magnetic Resonance Bank, and the Electron Microscopy Data Bank. Data safety and security and periodic archival updates are the primary responsibility of three wwPDB-designated Archive Keepers, including RCSB PDB for the Protein Data Bank, BMRB for the Biological Magnetic Resonance Bank, and EMDB for the Electron Microscopy Data Bank.

The wwPDB acknowledges the importance of global equity in the ability to deposit and access data, and the need for international involvement and collaboration in maintaining the wwPDB Core Archives.

The renewed wwPDB Charter describes the Associate Membership program, wherein Associate Members are expected to contribute to some of the wwPDB activities (deposition, validation, biocuration, remediation, storage, dissemination of public-domain structural biology data stored in one or more wwPDB Core Archives). The responsibilities of an individual wwPDB Associate Member for deposition, validation, biocuration, remediation, storage, and/or dissemination of public-domain structural biology data stored in one or more wwPDB Core Archives must be agreed upon by all wwPDB Full Members.

At the discretion of wwPDB Full Members, an external organization may be invited to apply to become a wwPDB Associate Member, following preliminary discussions and successful completion of due diligence and demonstration of sufficient technical expertise, adequate infrastructure, and sustainable funding. The decision to admit a new wwPDB Associate Member must be by unanimous vote of the current Heads of the existing wwPDB Full Members, supported by a simple majority of the voting members of the wwPDB Advisory Committee.

Full details of the arrangement are provided in thewwPDB Charter (PDF).