June 2012

JBC structure papers to require validation reports from PDB

Variation of Fig. 4 from article by Garcin et al in the Jan. 13, 2012, issue of JBC: Structural and Mechanistic Insights into Unusual Thiol Disulfide Oxidoreductase, DOI 10.1074/jbc.M111.288316

Attention, structural biologists! The Journal of Biological Chemistry soon will have a new requirement: When you submit a manuscript with an X-ray protein structure, you also will need to submit a validation summary report from one of the three World Wide Protein Data Bank centers. The report summarizes the results of an analysis of experimental data and geometry of reported structures by the wwPDB. The report will be used by JBC reviewers to confirm the accuracy and quality of the structures.

The JBC is an important forum for structural biology. In 2010, the journal had the largest number of primary citations for structures deposited in wwPDB. The latest move comes after a yearlong series of discussions among JBC associate editors and an editorial published last December to ask reviewers, authors and readers whether validation reports should be requested. The overall response was a resounding yes, with many saying that the report submission should be mandatory.

JBC Editor-In-Chief Marty Fedor says this new requirement is consistent with the journal’s history of publishing high-quality structures. Fedor, who is based at The Scripps Research Institute, mentions the resistance of some biologists in 1978 when the JBC made it a requirement that structures be deposited into the PDB prior to manuscript submission. But now “no one can imagine going back to the days before PDB depositions were required,” she says. “We feel this new requirement is going to be a similar step along the same path of taking advantage of the tools available to curate these kinds of database depositions and making sure they meet certain standards of quality before they are disseminated to the community at large.”

JBC Associate Editor Norma Allewell, a structural biologist at the University of Maryland who wrote the JBC editorial, notes the reports will make the task of reviewers and editors easier and will ensure that structures reported in the JBC meet the standards of the scientific community. “While there is a possibility that this requirement may reduce the number of structural manuscripts submitted to the JBC, it ensures that those that are accepted merit publication in the JBC,” she says.

wwPDB member Helen Berman at Rutgers University says the organization is delighted by the JBC’s move. With the report in hand, a reviewer can “be assured that the technical aspects of the crystallographic determination are fine,” she says. In the cases in which errors are found, “at least the errors get caught early on in the process, and you don’t have a situation that a structure has to be retracted.”

The requirement will be implemented by the end of the summer and will be noted in the JBC’s instruction to authors.

  1. 1. http://www.jbc.org/site/home/editorials/macromolecular.xhtml 


Raj_MukhopadhyayRajendrani Mukhopadhyay (rmukhopadhyay@asbmb.org) is the senior science writer for ASBMB Today and the technical editor for The Journal of Biological Chemistry. Follow her on Twitter at @rajmukhop.

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