wwPDB statement on Retraction of UAB PDB entries
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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.
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Posted on behalf of wwPDB,
--Gerard Kleywegt
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Gerard Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
[log in to unmask] http://www.ebi.ac.uk/pdbe/
Secretary: Celia Copp [log in to unmask]
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