Validation of Structures in the Protein Data Bank

Swanand Gore, Eduardo Sanz García, Pieter M.S. Hendrickx, Aleksandras Gutmanas, John D. Westbrook, Huanwang Yang, Zukang Feng, Kumaran Baskaran, John M. Berrisford, Brian P. Hudson, Yasuyo Ikegawa, Naohiro Kobayashi, Catherine L. Lawson, Steve Mading, Lora Mak, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Ezra Peisach, Gaurav SahniMonica R. Sekharan, Sanchayita Sen, Chenghua Shao, Oliver S. Smart, Eldon L. Ulrich, Reiko Yamashita, Martha Quesada, Jasmine Y. Young, Haruki Nakamura, John L. Markley, Helen M. Berman, Stephen K. Burley, Sameer Velankar, Gerard J. Kleywegt

Research output: Contribution to journalArticlepeer-review

102 Scopus citations

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. 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.

Original languageEnglish (US)
Pages (from-to)1916-1927
Number of pages12
JournalStructure
Volume25
Issue number12
DOIs
StatePublished - Dec 5 2017

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • 3D macromolecular structure
  • PDB
  • biocuration
  • data archiving
  • data deposition
  • structural biology
  • structure data quality
  • validation
  • wwPDB

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