The archiving and dissemination of biological structure data

Helen M Berman¹, Stephen K Burley², Gerard J Kleywegt³, John L Markley⁴, Haruki Nakamura⁵, Sameer Velankar³

Affiliations

¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA. Electronic address: berman@rcsb.rutgers.edu.
² Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
³ Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.
⁴ Biological Magnetic Resonance Bank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
⁵ Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

PMID: 27450113
PMCID: PMC5161703
DOI: 10.1016/j.sbi.2016.06.018

Review

The archiving and dissemination of biological structure data

Helen M Berman et al. Curr Opin Struct Biol. 2016 Oct.

. 2016 Oct:40:17-22.

doi: 10.1016/j.sbi.2016.06.018. Epub 2016 Jul 21.

Authors

Helen M Berman¹, Stephen K Burley², Gerard J Kleywegt³, John L Markley⁴, Haruki Nakamura⁵, Sameer Velankar³

Affiliations

¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA. Electronic address: berman@rcsb.rutgers.edu.
² Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
³ Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.
⁴ Biological Magnetic Resonance Bank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
⁵ Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

PMID: 27450113
PMCID: PMC5161703
DOI: 10.1016/j.sbi.2016.06.018

Abstract

The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.

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Figures

**Figure 1**
Growth of the PDB archive. A) Number of entries deposited annually (dark grey) and available at the end of each year (light grey); B) number of X-ray crystal structures, C) NMR structures, and D) 3DEM structures available each year.

**Figure 2**
wwPDB Deposition, Annotation, and Validation pipeline. Each box represents a modular component of the data processing workflow.

See this image and copyright information in PMC

References

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The archiving and dissemination of biological structure data

Affiliations

The archiving and dissemination of biological structure data

Authors

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources