wwPDB

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The wwPDB provides depositors with detailed reports (PDF and XML files) that include the results of model and experimental data validation, as part of the curation of all entries.


As these wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, the wwPDB partners strongly encourage journal editors and referees to request them from authors as part of the manuscript submission and review process. The reports are date-stamped and display the logo of the wwPDB site where the entry was curated. They contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by eLife, The Journal of Biological Chemistry, and the International Union of Crystallography (IUCr) journals as part of their manuscript-submission process.


The validation reports continue to be developed and improved as we receive recommendations from the expert Validation Task Forces (VTF) for X-ray, NMR, and EM, as we develop the wwPDB Deposition & Annotation (D&A) system, and as we collect feedback from depositors and users.


The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At many stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.


Official wwPDB validation reports provide both overall quality scores for a PDB submission and detailed lists of specific issues. Above-average global scores can sometimes mask local issues; hence it is important to review the entire report, especially during structure refinement.


The reports are provided as human-readable PDF files and as machine-readable XML files, and are made available with the public release of the corresponding PDB entry. The machine-readable files contain all of the detailed validation information and statistics. For example, the validation XML file specifies for each protein residue any outlying bond length or bond angle, the residue's rotameric state, its region in a Ramachandran plot, any atoms involved in too-close contacts, and (for X-ray structures) the fit to electron density. These XML files can be read and interpreted by popular visualization software packages, such as Coot, to display validation information for any publicly available PDB entry.

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