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Worldwide Protein Data Bank validation information: usage and trends.

Oliver S Smart¹, Vladimír Horský², Swanand Gore¹

¹Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.

Acta Crystallographica. Section D, Structural Biology

|March 14, 2018

Summary

The Worldwide Protein Data Bank (wwPDB) developed a validation pipeline to assess biomolecular structure quality. This system combines metrics into an overall score for ranking structures and analyzing trends.

Keywords:

PDB Protein Data Bank X-ray crystallography quality control three-dimensional macromolecular structure validation

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Area of Science:

Structural Biology
Biochemistry
Bioinformatics

Background:

Assessing the quality of biomolecular structures in the Protein Data Bank (PDB) is crucial for scientific integrity.
The Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to define standards for structure validation.
Existing validation methods needed integration into a unified pipeline for deposition, biocuration, and validation.

Purpose of the Study:

To present the integrated wwPDB validation pipeline for biomolecular structures.
To demonstrate how validation metrics can be combined to create an overall quality score.
To introduce the ValTrends^DB database for analyzing structure properties and validation trends.

Main Methods:

Development of a comprehensive validation pipeline by wwPDB partners.
Integration of the pipeline into the wwPDB OneDep system.
Creation of the ValTrends^DB database for accessing and analyzing X-ray crystal structure data.

Main Results:

The wwPDB validation pipeline provides standardized quality assessment for PDB entries.
A combined validation score enables ranking of macromolecular structures and domains.
ValTrends^DB facilitates the analysis of trends and correlations in structure properties and validation metrics.

Conclusions:

The wwPDB validation pipeline and scoring system enhance the reliability of deposited biomolecular structures.
The wwPDB Validation Service webserver offers pre-deposition quality checks.
ValTrends^DB serves as a valuable resource for researchers studying structure quality and trends.