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Validation of Structures in the Protein Data Bank.

Authors
  • Gore, Swanand1
  • Sanz García, Eduardo1
  • Hendrickx, Pieter M S1
  • Gutmanas, Aleksandras2
  • Westbrook, John D3
  • Yang, Huanwang3
  • Feng, Zukang3
  • Baskaran, Kumaran4
  • Berrisford, John M1
  • Hudson, Brian P3
  • Ikegawa, Yasuyo5
  • Kobayashi, Naohiro5
  • Lawson, Catherine L3
  • Mading, Steve4
  • Mak, Lora1
  • Mukhopadhyay, Abhik1
  • Oldfield, Thomas J1
  • Patwardhan, Ardan1
  • Peisach, Ezra3
  • Sahni, Gaurav1
  • And 14 more
  • 1 Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • 2 Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address: [email protected]
  • 3 RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. , (Jersey)
  • 4 BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
  • 5 PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan. , (Japan)
  • 6 RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA. , (Jersey)
Type
Published Article
Journal
Structure
Publisher
Elsevier
Publication Date
Dec 05, 2017
Volume
25
Issue
12
Pages
1916–1927
Identifiers
DOI: 10.1016/j.str.2017.10.009
PMID: 29174494
Source
Medline
Keywords
License
Unknown

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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