Retractions and Fraud

From Proteopedia

Fraudulent or erroneous structures usually take many years to be removed from the PDB, and some remain uncorrected ^{[1] [2] [3]}.

Problematic PDB entries that need to be addressed in a future revision of the article below are documented in ^{[1] [2] [3] [4] [5]}.

A number of PDB entries have been retracted^[6], either due to fraud or honest mistakes. Retractions can be searched for at the Retraction Database of RetractionWatch.com, which also contains Corrections and Expressions of Concern. Concerns about published structures may also be expressed at the post-publication peer review site PubPeer.com.

Some historic errors and clearly incorrect PDB depositions are described by Wlodawer et al., 2008^[7].

• 2019, February: The history and results of the fraud findings for H. Krishna Murthy (see 2009 below) are summarized in Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures, Paper Retractions^[8].
• 2016, April: Nature formally retracts 2hr0^[9]. See 2009 below.

• 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^[10]. 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. Ahvazi was subsequently employed as a US patent examiner.

• 2012, February: 3k78 was removed from the PDB because it appears to be fraudlent^[11][12]. Subsequently, Robert Schwarzenbacher confessed to data fabrication, and was fired from his position at the University of Salzburg in Austria^[13]. In April 2013, the Journal of Immunology retracted the crystallographic results in the original 2010 article^[14].

• 2012, January: 2hlb was retracted by the authors^[15].

• 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^[6] and the discussion of fraud^[16] on the PDB email list, and Fraud rocks protein community in Nature^[17]. An official statement by the University of Alabama^[18] recommended retraction of 1bef, 1cmw, 1df9, 2qid, 1g40, 1g44, 1l6l, 2ou1, 1rid, 1y8e, 2a01, and 2hr0 (see 2016 above for the formal retraction of 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. See also the Office of Research Integrity Misconduct Review Results^[8] under 2019 above.

• 2007: Geoffrey Chang^[19] and colleagues retracted five PDB entries^[20][21]. The structures had major errors originating in part from an error in one of the software programs used^[22]. 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^[23] 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^[24]] for the single model refinement of MsbA but were discounted ...." (Quotations from Matthews, 2007^[23])

See Also

• Quality assessment for molecular models
• Structural biology corrections highlight best of the scientific process by Jeffrey Perkel, 2016.
• Searchable Retraction Database of RetractionWatch.com.
• Post-publication reviews at PubPeer.com.

References

1. ↑ ^{1.0 1.1} Rupp B, Wlodawer A, Minor W, Helliwell JR, Jaskolski M. Correcting the record of structural publications requires joint effort of the community and journal editors. FEBS J. 2016 Dec;283(24):4452-4457. doi: 10.1111/febs.13765. Epub 2016 Jun 10. PMID:27229767 doi:http://dx.doi.org/10.1111/febs.13765
2. ↑ ^{2.0 2.1} Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B. Detect, Correct, Retract: How to manage incorrect structural models. FEBS J. 2017 Nov 7. doi: 10.1111/febs.14320. PMID:29113027 doi:http://dx.doi.org/10.1111/febs.14320
3. ↑ ^{3.0 3.1} Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B. Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. IUCrJ. 2014 Apr 14;1(Pt 3):179-93. doi: 10.1107/S2052252514005442. eCollection, 2014 May 1. PMID:25075337 doi:http://dx.doi.org/10.1107/S2052252514005442
4. ↑ Stanfield R, Pozharski E, Rupp B. Comment on Three X-ray Crystal Structure Papers. J Immunol. 2016 Jan 15;196(2):521-4. doi: 10.4049/jimmunol.1501343. PMID:26747564 doi:http://dx.doi.org/10.4049/jimmunol.1501343
5. ↑ Stanfield R, Pozharski E, Rupp B. Additional Comment on Three X-ray Crystal Structure Papers. J Immunol. 2016 Jan 15;196(2):528-30. doi: 10.4049/jimmunol.1502281. PMID:26747567 doi:http://dx.doi.org/10.4049/jimmunol.1502281
6. ↑ ^{6.0 6.1} wwPDB Statement on Retraction of PDB Entries.
7. ↑ Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J. 2008 Jan;275(1):1-21. doi: 10.1111/j.1742-4658.2007.06178.x. Epub 2007, Nov 23. PMID:18034855 doi:http://dx.doi.org/10.1111/j.1742-4658.2007.06178.x
8. ↑ ^{8.0 8.1} Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures, Paper Retractions.
9. ↑ Abdul Ajees A, Volanakis JE, Narayana SV. Retraction: The structure of complement C3b provides insights into complement activation and regulation. Nature. 2016 Apr 14;532(7598):268. doi: 10.1038/nature16523. Epub 2016 Jan 4. PMID:26727161 doi:http://dx.doi.org/10.1038/nature16523
10. ↑ Case Summary: Ahvazi, Bijan. Office of Research Integrity, October 2014.
11. ↑ Abbott A. Trial tests Austrian integrity body. Nature. 2012 May 1;485(7396):15. doi: 10.1038/485015a. PMID:22552066 doi:10.1038/485015a
12. ↑ Protein structure retracted after investigation into “highly improbable features,” journal calls it fraud, April 2012
13. ↑ Retraction Watch: Archive for Robert Schwarzenbacher.
14. ↑ Correction: Antigen aggregation decides the fate of the allergic immune response.
15. ↑ Retraction of 2hlb by PNAS.
16. ↑ Discussion of fraud on the PDB email list.
17. ↑ 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
18. ↑ 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.
19. ↑ See Geoffrey Chang at Wikipedia.
20. ↑ 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
21. ↑ Summary of Miller article in Science (previous citation)
22. ↑ 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.
23. ↑ ^{23.0 23.1} 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
24. ↑ 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