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Evidently Gerard Kleywegt was right when he said "there is no way of keeping even highly suspicious models out of the public database (or of evicting them)" [ http://journals.iucr.org/d/issues/2009/02/00/ba5123/index.html]. We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? Granted, "validation is crucial for both the producers and the consumers of biomacromolecular structures and validation tools should be used both to assess the overall quality of a model and to assess the reliability of particularly interesting aspects" [Ibid]. Still, I can't say I'm comfortable with just leaving such structures in the PDB with nary a "caveat emptor". What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp <[log in to unmask]<https://mail.google.com/mail/?view=cm&fs=1&tf=1&[log in to unmask]> > wrote: > >which structure ended up as number 100.000? > I guess that depends if we still count the Murthy corpses like 2a01 This > 3-armed Swastika for example still does not come with a single warning > short of a poor quality report > http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, > sorry, 99990 (or less….) valid entries only at the time of announcement. > > Cheers, BR > > > > Supplemental material: > > > > “The PDB says it will remove the other ten structures only when editors at > the journals in which they were originally published or the authors > themselves retract them” > > *http://www.nature.com/news/2009/091222/full/462970a.html > <http://www.nature.com/news/2009/091222/full/462970a.html>* > > > > > > “With the support of the structural-biology community, the mission of the > wwPDB is to safeguard the integrity and improve the quality of the PDB > archive.” > > http://www.nature.com/nature/journal/v463/n7280/full/463425c.html > > > > Not to be overly cynical, but > > > > http://tinyurl.com/pmupalt > > > > > > *From:* CCP4 bulletin board [mailto:[log in to unmask]<https://mail.google.com/mail/?view=cm&fs=1&tf=1&[log in to unmask]>] > *On Behalf Of *mesters > *Sent:* Mittwoch, 14. Mai 2014 14:42 > *To:* [log in to unmask]<https://mail.google.com/mail/?view=cm&fs=1&tf=1&[log in to unmask]> > > *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone > > > > Amazing, great! > > And, which structure ended up as number 100.000? > > - J. - > > > Am 14.05.14 10:42, schrieb battle: > > The Worldwide Protein Data Bank (wwPDB) organization is proud to announce > that the Protein Data Bank archive now contains more than 100,000 entries. > > Established in 1971, this central, public archive of > experimentally-determined protein and nucleic acid structures has reached a > critical milestone thanks to the efforts of structural biologists > throughout the world. > > Read the full story at: > http://www.wwpdb.org/news/news_2014.html#13-May-2014 > > -- > Gary Battle > on behalf on the wwPDB > > > > -- > Dr. Jeroen R. Mesters > Deputy, Senior Researcher & Lecturer > > Institute of Biochemistry, University of Lübeck > Ratzeburger Allee 160, 23538 Lübeck, Germany > > phone: +49-451-5004065 (secretariate 5004061) > fax: +49-451-5004068 > > http://www.biochem.uni-luebeck.de <Http://www.biochem.uni-luebeck.de> > http://www.iobcr.org <Http://www.iobcr.org> > > > -- > If you can look into the seeds of time and tell which grain will grow and > which will not, speak then to me who neither beg nor fear (Shakespeare's > Macbeth, Act I, Scene 3) > -- > > > > > *Disclaimer * This message contains confidential information and is > intended only for the individual named. If you are not the named addressee > you should not disseminate, distribute or copy this e-mail. 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