Validation of Structures in the Protein Data Bank

Area of Science:

• Structural Biology
• Biocuration
• Data Validation

Background:

• The Worldwide Protein Data Bank (wwPDB) developed OneDep, a unified system for data deposition, biocuration, and validation.
• Validation reports are generated at multiple stages of data processing within OneDep.

Purpose of the Study:

• To introduce the OneDep system and its validation reporting capabilities.
• To highlight the importance of validation reports for assessing macromolecular structure quality.

Main Methods:

• OneDep integrates recommendations from expert task forces in crystallography, nuclear magnetic resonance, and cryoelectron microscopy.
• Validation reports provide metrics on experimental data, structural models, and their fit.
• The validation module is accessible as a web server and a web service.

Main Results:

• OneDep produces validation reports for three-dimensional structures of biological macromolecules.
• These reports offer depositors crucial metrics for evaluating structure quality.
• Geometric quality scores for proteins in the PDB archive show improvement over the last decade.

Conclusions:

• OneDep enhances the deposition, biocuration, and validation process for macromolecular structures.
• wwPDB validation reports are increasingly required by journals and are part of the public PDB archive.
• The system contributes to the overall improvement of structural data quality in the PDB.