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 Sahni; Monica 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; Rutgers Univ., Piscataway, NJ (United States)

doi:10.1016/j.str.2017.10.009

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Validation of Structures in the Protein Data Bank

Journal article

Open access

Peer reviewed

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, …

Structure (London), Vol.25(12), pp.1916-1927

12/05/2017

DOI: https://doi.org/10.1016/j.str.2017.10.009

PMCID: PMC5718880

PMID: 29174494

Abstract

3D macromolecular structure

biocuration

data archiving

data deposition

PDB

structural biology

structure data quality

validation

wwPDB

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. [Display omitted] •Validation reports are available for X-ray, NMR, and EM structures in the PDB•Preliminary reports obtained at deposition, stand-alone servers, and programmatically•Official reports from biocuration should be submitted with manuscripts•Quality metrics for protein structures 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.

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Title: Validation of Structures in the Protein Data Bank
Creators: Swanand Gore - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Eduardo Sanz García - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Pieter M.S Hendrickx - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Aleksandras Gutmanas - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
John D Westbrook - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Huanwang Yang - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Zukang Feng - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Kumaran Baskaran - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
John M Berrisford - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Brian P Hudson - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Yasuyo Ikegawa - PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
Naohiro Kobayashi - PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
Catherine L Lawson - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Steve Mading - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
Lora Mak - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Abhik Mukhopadhyay - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Thomas J Oldfield - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Ardan Patwardhan - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Ezra Peisach - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Gaurav Sahni - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Monica R Sekharan - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Sanchayita Sen - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Chenghua Shao - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Oliver S Smart - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Eldon L Ulrich - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
Reiko Yamashita - PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
Martha Quesada - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Jasmine Y Young - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Haruki Nakamura - PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
John L Markley - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
Helen M Berman - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Stephen K Burley - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Sameer Velankar - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Gerard J Kleywegt - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Rutgers Univ., Piscataway, NJ (United States)
Publication Details: Structure (London), Vol.25(12), pp.1916-1927
Date published: 12/05/2017
Publisher: Elsevier Ltd
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine
Language: English
Resource Type: Journal article
Identifiers: 991031666032004646