Following an announcement last week from the University of Alabama at Birmingham that a former UAB researcher may have fabricated data about protein structures that are contained in the Protein Data Bank, the PDB said this week that it has "made obsolete" one of 12 protein questionable structures.
The Worldwide Protein Data Bank, or wwPDB, which coordinates PDB data in the US, Europe, and Japan, said in a statement this week that it has removed one of the structures, that of the dengue virus NS3 serine protease published in the Journal of Biological Chemistry in 1999, because the journal has retracted the paper.
"The JBC editors requested that the Protein Data Bank entry described in that paper (PDB code 1BEF) be made obsolete and this request has been granted," wwPDB said.
In its announcement last week, the university requested that the PDB remove a total of 12 structures published by former UAB researcher H.M. Krishna Murthy, noting that it had re-analyzed each structure alleged to have been fabricated and found " a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than not falsified and/or fabricated." [BioInform 12-11-2009]
UAB requested that these structures described in 10 journal publications and 12 PDB entries, be "removed from the public record."
The wwPDB explained this week that under its policy, entries can only "be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors)."
The employer of an author may request that a PDB entry be removed, wwPDB said, "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 "ensures both due process and the scientific integrity of the worldwide structural archive," wwPDB said.
In line with this policy, wwPDB said that it "will make the remaining 11 entries obsolete if and when the corresponding papers are retracted."