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wwPDB Statement on Retraction of PDB Entries

In its December 4, 2009 issue, the Journal of Biological Chemistry (JBC) retracted an article by H.M. Krishna Murthy et al. describing the structure of dengue virus NS3 serine protease published 10 years earlier (http://www.jbc.org/content/284/49/34468.full). The JBC editors requested that the Protein Data Bank (PDB) entry described in that paper (PDB code 1BEF) be made obsolete and this request has been granted.

It is the current wwPDB (Worldwide PDB) policy that entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). Typically, authors themselves request an entry to be made obsolete because they have collected better experimental data or produced an improved interpretation of the existing data. In addition, the employer of an author may request this, but in that case the request must be fully documented and a retraction published in the journal that published the original paper describing the entry. This policy mirrors the manner in which Bell Labs/Lucent handled the case of its employee J.H. Schon (see http://en.wikipedia.org/wiki/Jan_Hendrik_Schon) and it ensures both due process and the scientific integrity of the worldwide structural archive.

Earlier this month, the University of Alabama at Birmingham (UAB) announced on its website ( http://main.uab.edu/Sites/reporter/articles/71570/) its plans to retract 12 PDB entries and 10 papers (including the one in JBC), although the case against the scientist involved is still being investigated by the Office for Research Integrity (ORI; http://ori.dhhs.gov/). In line with its current policy, wwPDB will make the remaining 11 entries obsolete if and when the corresponding papers are retracted.

The PDB is a historical archive that stores, annotates and disseminates structure models and their related experimental data (deposition of which has been mandatory since February 2008). wwPDB has convened expert, community-driven Validation Task Forces for X-ray (in 2008) and NMR (in 2009) to advise on the most suitable criteria to use for validating structure entries (model, data and fit of model to data) when they are deposited. The recommendations of these task forces will be implemented as part of the deposition and annotation procedures of the wwPDB partners. Moreover, it is envisioned that the results of these validation procedures will be captured in a report that will be sent to the depositors and can be transmitted by them to the journal to which the corresponding manuscript is submitted. Availability of such a report would greatly facilitate assessment of the reliability of structural data and its interpretation by journal editors and referees alike. wwPDB hopes that eventually all journals that publish structural data on biological macromolecules will make submission of the PDB validation report mandatory. The continuing mission of the wwPDB partners is to safeguard the integrity and improve the quality of the structural archive, with the enthusiastic support of the international structural biology community.

The Worldwide Protein Data Bank (wwPDB; http://www.wwpdb.org/) consists of organisations that act as deposition, data-processing and distribution centres for PDB data. The members are the RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and the BMRB (USA). The mission of the wwPDB is to maintain a single Protein Data Bank archive of macromolecular structural data that is freely and publicly available to the global community.


December 17, 2009



Updated February 2, 2010

For additional information, see Safeguarding the integrity of protein archive Nature (2010) 463:425. doi:10.1038/463425c


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