Retractions and Fraud

From Proteopedia

Revision as of 23:17, 15 November 2014

A number of PDB entries have been retracted, either due to fraud or honest mistakes^[1].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

• 2012, February: 3k78 was removed from the PDB because it appears to be fraudlent^[3][4].

• 2009 and subsequently, several entries authored by H.M. Krishna Murthy were removed from the PDB as they appear to be fraudulent. Those already removed, as well as those for which removal is pending, are listed at Murthy fraud. See also this list of possibly fraudlent entries co-authored by Murthy. See the statement by the Worldwide PDB^[1] and the discussion of fraud^[5] on the PDB email list and the official statement by the University of Alabama^[6]

• 2007: Geoffrey Chang^[7] and colleagues retracted five PDB entries^[8][9]. The structures had major errors originating in part from an error in one of the software programs used^[10]. 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^[11] 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^[12]] for the single model refinement of MsbA but were discounted ...." (Quotations from Matthews, 2007^[11])

See Also

• Quality assessment for molecular models

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. ↑ Discussion of fraud on the PDB email list.
6. ↑ Official statement by the University of Alabama on fraudlent PDB entries by H. M. Krishna Murthy . This statement includes detailed information about the analysis of each entry by outside experts.
7. ↑ See Geoffrey Chang at Wikipedia.
8. ↑ 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
9. ↑ Summary of Miller article in Science (previous citation)
10. ↑ 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.
11. ↑ ^{11.0 11.1} 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
12. ↑ 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