Validation of Structures in the Protein Data Bank

Swanand Gore(European Bioinformatics Institute), Eduardo Sanz‐García(European Bioinformatics Institute), P. Hendrickx(European Bioinformatics Institute), Aleksandras Gutmanas(European Bioinformatics Institute), John Westbrook(Rutgers, The State University of New Jersey), Huanwang Yang(Rutgers, The State University of New Jersey), Zukang Feng(Rutgers, The State University of New Jersey), Kumaran Baskaran(University of Wisconsin–Madison), John M. Berrisford(European Bioinformatics Institute), Brian P. Hudson(Rutgers, The State University of New Jersey), Yasuyo Ikegawa(Protein Research Foundation), Naohiro Kobayashi(Protein Research Foundation), Catherine L. Lawson(Rutgers, The State University of New Jersey), Steve Mading(University of Wisconsin–Madison), Lora Mak(European Bioinformatics Institute), Abhik Mukhopadhyay(European Bioinformatics Institute), Thomas J. Oldfield(European Bioinformatics Institute), Ardan Patwardhan(European Bioinformatics Institute), Ezra Peisach(Rutgers, The State University of New Jersey), Gaurav Sahni(European Bioinformatics Institute), Monica Sekharan(Rutgers, The State University of New Jersey), Sanchayita Sen(European Bioinformatics Institute), Chenghua Shao(Rutgers, The State University of New Jersey), Oliver S. Smart(European Bioinformatics Institute), Eldon L. Ulrich(University of Wisconsin–Madison), Reiko Yamashita(Protein Research Foundation), Martha Quesada(Rutgers, The State University of New Jersey), Jasmine Young(Rutgers, The State University of New Jersey), Haruki Nakamura(Protein Research Foundation), John L. Markley(University of Wisconsin–Madison), Helen M. Berman(Rutgers, The State University of New Jersey), S.K. Burley(Rutgers, The State University of New Jersey), Sameer Velankar(European Bioinformatics Institute), Gerard J. Kleywegt(European Bioinformatics Institute)
Structure
November 23, 2017
10.1016/j.str.2017.10.009
Cited by 294Open Access
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Abstract

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.

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