Retractions and Fraud

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A number of PDB entries have been retracted, either due to fraud or honest mistakes[1].

  • 2014, October: Bijan Ahvazi, formerly the Director of the Laboratory of X-ray Crystallography, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, USA, was found to have falsified data in several publications[2]. Ahvazi is the sole author for PDB entries 1l9m, 1l9n, 1nud, 1nug, 1nuf, first author of 1eyy, 1ez0, and coauthor of 1yue, 1tg6, and 1by4.
  • 2012, February: 3k78 was removed from the PDB because it appears to be fraudlent[3][4]. Subsequently, Robert Schwarzenbacher confessed to data fabrication, and was fired from his position at the University of Salzburg in Austria[5]. In April 2013, the Journal of Immunology retracted the crystallographic results in the original 2010 article[6].
  • 2012, January: 2hlb was retracted by the authors[7].
  • 2009, December: Several entries authored by H.M. Krishna Murthy were removed from the PDB as they appear to be fraudulent. See the statement by the Worldwide PDB[1] and the discussion of fraud[8] on the PDB email list, and Fraud rocks protein community in Nature[9]. An official statement by the University of Alabama[10] recommended retraction of 1bef, 1cmw, 1df9, 2qid, 1g40, 1g44, 1l6l, 2ou1, 1rid, 1y8e, 2a01, and 2hr0. This statement includes detailed information about the analysis of each entry by outside experts. In addition, the reliability of 1bgx, 1ay1, 1hef, 1heg, 1sbg, 1hps, and 1hos have been called into question since they were co-authored by H. M. Krishna Murthy.
  • 2007: Geoffrey Chang[11] and colleagues retracted five PDB entries[12][13]. The structures had major errors originating in part from an error in one of the software programs used[14]. When the errors came to light, the authors immediately admitted the problem and retracted the affected publications. The retracted structures were 1jsq, 1pf4, 1z2r, 1s7b, and 2f2m. Brian Matthews[15] explains that it should have been immediately clear that the electron density maps were incorrect:
"If F+ and F− are interchanged, there are situations in which an inverted electron density map could result, but obtaining such a map should immediately signal that an error had occurred." "Where anomalous scattering data are included, as for the MsbA structure determination, the situation should never arise that one would need to choose between the correct map and its inverted image." "Extraordinarily high values of R and Rfree were obtained [by Chang and Roth, 2001[16]] for the single model refinement of MsbA but were discounted ...." (Quotations from Matthews, 2007[15])


See Also

References

  1. 1.0 1.1 wwPDB Statement on Retraction of PDB Entries.
  2. Case Summary: Ahvazi, Bijan. Office of Research Integrity, October 2014.
  3. Abbott A. Trial tests Austrian integrity body. Nature. 2012 May 1;485(7396):15. doi: 10.1038/485015a. PMID:22552066 doi:10.1038/485015a
  4. Protein structure retracted after investigation into “highly improbable features,” journal calls it fraud, April 2012
  5. Retraction Watch: Archive for Robert Schwarzenbacher.
  6. Correction: Antigen aggregation decides the fate of the allergic immune response.
  7. Retraction of 2hlb by PNAS.
  8. Discussion of fraud on the PDB email list.
  9. Borrell B. Fraud rocks protein community. Nature. 2009 Dec 24;462(7276):970. doi: 10.1038/462970a. PMID:20033014 doi:http://dx.doi.org/10.1038/462970a
  10. Official statement by the University of Alabama on fraudlent PDB entries by H. M. Krishna Murthy. Thanks to User:Peter A. Keller for providing this updated link on May 16, 2014.
  11. See Geoffrey Chang at Wikipedia.
  12. Miller G. Scientific publishing. A scientist's nightmare: software problem leads to five retractions. Science. 2006 Dec 22;314(5807):1856-7. PMID:17185570 doi:10.1126/science.314.5807.1856
  13. Summary of Miller article in Science (previous citation)
  14. Jeffrey, Philip D., Analysis of errors in the structure determination of MsbA (open access). Acta Crystallogr D Biol Crystallogr. 2009 February 1; 65(Pt 2): 193–199. doi: 10.1107/S0907444909001292.
  15. 15.0 15.1 Matthews BW. Five retracted structure reports: inverted or incorrect? Protein Sci. 2007 Jun;16(6):1013-6. Epub 2007 May 1. PMID:17473006 doi:10.1110/ps.072888607
  16. Chang G, Roth CB. Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters. Science. 2001 Sep 7;293(5536):1793-800. PMID:11546864 doi:10.1126/science.293.5536.1793

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