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Title: Validation of Structures in the Protein Data Bank

Journal Article · · Structure
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  1. European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom). European Bioinformatics Inst. (ELBL-EBI). Protein Data Bank in Europe (PDBe). Wellcome Genome Campus
  2. Rutgers Univ., Piscataway, NJ (United States). Center for Integrative Proteomics Research. RCSB Protein Data Bank
  3. Univ. of Wisconsin, Madison, WI (United States). BioMagResBank (BMRB)
  4. European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom). European Bioinformatics Inst. (ELBL-EBI). Protein Data Bank in Europe (PDBe). Wellcome Genome Campus
  5. Osaka Univ. (Japan). Inst. for Protein Research. PDBj
  6. Rutgers Univ., Piscataway, NJ (United States). Center for Integrative Proteomics Research. RCSB Protein Data Bank; Univ. of California, La Jolla, CA (United States). Sand Diego Supercomputer Center. RCSB Protein Data Bank; Univ. of California, La Jolla, CA (United States). Skaggs School of Pharmacy and Pharmaceutical Sciences; Rutgers Univ., Piscataway, NJ (United States). Inst. for Quantitative Biomedicine

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.

Research Organization:
Rutgers Univ., Piscataway, NJ (United States)
Sponsoring Organization:
USDOE Office of Science (SC); USDOE
Grant/Contract Number:
FG02-00ER41132; DBI-1338415
OSTI ID:
1410138
Alternate ID(s):
OSTI ID: 1623723
Journal Information:
Structure, Vol. 25, Issue 12; ISSN 0969-2126
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

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A probabilistic approach for validating protein NMR chemical shift assignments journal May 2010
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A New Generation of Crystallographic Validation Tools for the Protein Data Bank journal October 2011
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RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy journal October 2018
Protein Data Bank: the single global archive for 3D macromolecular structure data journal October 2018
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Figures / Tables (8)