Validation of Structures in the Protein Data Bank

Summary The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various 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.
Graphical Abstract
Highlights • Validation reports are available for X-ray, NMR, and EM structures in the PDB • Preliminary reports obtained at deposition, stand-alone servers, and programmatically • Official reports from biocuration should be submitted with manuscripts • Quality metrics for protein structures have improved over the past decade
Gore et al. describe the community-recommended validation reports, produced by wwPDB at deposition and biocuration of PDB submissions, and integrated into the archive of publicly released PDB entries. The authors also show that the quality of protein structures has improved over the last decade.