Data Deposition/Biocuration Services and Archive Management

Deposition Statistics

In the second quarter of 2018, 3172 experimentally-determined structures were deposited to the archive for a total of 6143 structure deposited in the year. Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

Of the structures deposited in 2018 so far, 88.2% were deposited with a release status of hold until publication; 7.8% were released as soon as annotation of the entry was complete; and 4.0% were held until a particular date.

88.3% of these entries were determined by X-ray crystallographic methods; 4.0% by NMR methods; and 7.1% by 3DEM.

During the same period, 2629 structures and 348 EMDB maps were released in the PDB.

Improvements to Data Replacement Prior to Release

The OneDep process of replacing PDB and EMDB data prior to release has improved. All new data are checked and validated before the new files are merged into the deposition session, and a new validation report is provided. The new report should be carefully reviewed, particularly for highlighted issues, and approved prior to re-submission. Any major data errors or data inconsistencies between versions are displayed for review and correction.

These changes ensure that previous data are not accidentally removed and also enable more efficient biocuration due to the reduction of file replacement errors. Overall, these changes should improve the quality of the data and the transparency of the file replacement process.

Privacy Policy Update

wwPDB is making sure that we are open and clear about how we handle personal data in OneDep. We have updated the wwPDB privacy policy to comply with the changes brought by the European Union data protection law (GDPR).  If you have any questions about this privacy policy, please send them to deposit-help@mail.wwpdb.org.

ORCIDs To Become Mandatory for OneDep Contact Authors

The wwPDB OneDep system for deposition, validation and biocuration will require contact authors to provide their unique ORCID identifiers when preparing depositions later this summer. This change will enable wwPDB efforts to correctly attribute PDB structures to contact authors.  At a later point, ORCID will be used to authenticate and reorganize access to deposition data within OneDep.

Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures

In 2018, The Office of Research Integrity (ORI) of the U.S. Department of Health and Human Services announced their final Research Misconduct Finding in the case of H.M. Krishna Murthy. It was found that Murthy reported Falsified and/or fabricated research in 10 journal publications and 12 corresponding PDB structures. While the ORI was gathering and evaluating evidence in this case, 5 Murthy structures in the PDB were obsoleted in accord with wwPDB policies in response to retraction of 4 journal publications. In response to a formal request from ORI received on April 23, 2018, the remaining 7 Murthy structures in the PDB were obsoleted, again in accord with wwPDB policies. ORI conduct of its investigations is designed to ensure due process for individuals accused of research misconduct, and strict confidentiality is maintained throughout. Only findings of research misconduct are made public.

In December 2009, the University of Alabama at Birmingham (UAB) announced that it planned to retract 12 PDB entries and 10 related publications authored by H.M. Krishna Murthy, in his capacity as Principal Investigator and UAB employee. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, 5 of the structures were obsoleted upon retraction of the related publications by the journals. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, the remaining 7 structures were obsoleted upon receipt of the ORI request.  A detailed PDB history of this case is available.

Structure Validation and the Role of the PDB as an Archival Data Resource

The PDB is an archival resource that stores, annotates, and disseminates structure models and their related experimental data. The wwPDB has convened expert, community-driven Validation Task Forces for X-ray (in 2008), NMR (in 2009), and (in collaboration with the EMDataBank) Cryo-EM (in 2010) to advise on the most suitable criteria to use for validating structure entries (model, experimental data, and fit of model to data) when they are deposited. Recommendations of these validation task forces have been implemented as part of the wwPDB OneDep system for deposition, annotation, and validation of PDB structures.

The results of these wwPDB validation procedures are captured in a report that is provided to depositors and can be transmitted by them to the journal to which the corresponding manuscript is submitted. Availability of such a report greatly facilitates assessment of the reliability of structural data and its interpretation by journal editors and referees alike. The wwPDB has urged journals publishing structural data on biological macromolecules to require submission of the wwPDB validation report together with the manuscript. The continuing mission of the wwPDB partners is to safeguard the integrity and improve the quality of the structural archive, with the support of the international structural biology community.

For additional information, see

  1. Case Summary: Murthy, Krishna H.M.(2018) US Department of Health and Human Services, The Office of Research Integrity
  2. Findings of Research Misconduct Notice 2018-07782 (2018) Federal Register 83: 16370
  3. Berman, H. M., G. J. Kleywegt, H. Nakamura, J. L. Markley and S. K. Burley (2010). "Safeguarding the integrity of protein archive." Nature 463(7280): 425 doi: 10.1038/463425c.
  4. Baker, E. N., Z. Dauter, H. Einspahr and M. S. Weiss (2010). "In defence of our science--validation now!" Acta Crystallogr D Biol Crystallogr 66(Pt 2): 115 doi:10.1107/S1744309110001326