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Validating Macromolecular Structures

Open AccessPublished:January 01, 2012DOI:https://doi.org/10.1074/jbc.E111.000112
      Over the past decade, the Journal of Biological Chemistry (JBC) has become an important medium for reporting macromolecular structures determined by crystallography, nuclear magnetic resonance, and cryoelectron microscopy. In 2010, the JBC had the largest number of primary citations, 645, for structures deposited in the Worldwide Protein Data Bank (wwPDB; www.wwpdb.org).
      Many user communities—academic scientists, corporate R&D investigators, educators, clinicians, and intellectual property professionals—need the structures in the wwPDB for different purposes. For this reason, ensuring the quality of published structures has been a concern since the inception of the database known as the Protein Data Bank in 1971.
      In 2008, the wwPDB-appointed X-ray Validation Task Force (VTF) began discussions about developing new structure validation tools. The VTF recently delivered its final report, which emphasizes validation of bonding geometries; backbone and side-chain conformations; molecular packing, including atomic and molecular interactions; fit to experimental data; and quality of the experimental data (Read, R. J. et al. (2011) Structure 19, 1395–1412). Following the recommendation of the VTF, wwPDB will create a new validation suite to assess submitted structures and provide validation results, including a clear summary, to help depositors improve structures when necessary before wwPDB releases the coordinates.
      The validation summary report, which the wwPDB currently provides to depositors, may also be useful to journal editors and referees in assessing the quality of structural experiments. As a first step, the VTF report suggests that reviewers could ask editors to request the summary validation reports from authors if the reviewers think they would be useful. However, the VTF recommends that journals may ultimately want to require authors to submit the summary reports with their manuscripts.
      The International Union of Crystallography began to require authors to provide summary validation reports with manuscripts for its journals at the end of 2010. The Union reports that all authors were able to submit reports; there wasn't a noticeable reduction in the number of submitted articles; and this requirement was welcomed by authors, editors, and reviewers. Other journals, including Nature Structural & Molecular Biology ((2010) Nature Struct. Mol. Biol. 17, 917), are also considering adopting this policy.
      Because the JBC has become an important medium for reporting macromolecular structures, we must also consider how to proceed. The Journal already requires coordinates and structure factors to be deposited before publication. Should the Journal also encourage or require summary validation reports to be submitted along with manuscripts? In addition to being helpful to reviewers who have questions about the quality of reported structures or need more information from the validation reports, submission of those reports would also reduce the Journal's risk of publishing structures that are misleading, erroneous, or fraudulent.
      Before making a decision about how to proceed, JBC would like to hear from its authors and readers. Do you think the JBC should begin to request summary validation reports when reviewers suggest them? Do you think the JBC should require validation reports be submitted with manuscripts? Will the reports enhance the quality of the Journal? Please email us at [email protected] with your comments and suggestions. We look forward to hearing from you.
      This editorial reflects a consensus among the Editors and Associate Editors of the Journal of Biological Chemistry.