Open Access

Methods in Molecular Biology, pages 627-641

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

Stephen K. Burley ^{1, 2, 3}

Helen M. Berman ¹

Gerard J. KLEYWEGT ⁴

John L. Markley ⁵

Haruki Nakamura ⁶

Sameer Velankar ⁴

Hide authors affiliations Show authors affiliations: 6 affiliations

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics, Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, USA |

Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, USA |

Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, USA |

⁴

Protein Data Bank in Europe, European Molecular Biology Laboratory–European Bioinformatics Institute, Cambridge, UK |

⁵

BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, USA |

⁶

Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka, Japan |

Publication type: Book Chapter

Publication date: 2017-06-01

Springer Nature

Journal: Methods in Molecular Biology

Quartile SCImago

Quartile WOS

—

Impact factor: —

ISSN: 10643745, 19406029

DOI: 10.1007/978-1-4939-7000-1_26

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PubMed ID: 28573592

Abstract

The Protein Data Bank (PDB)––the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes––was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

By date By citations

Top-30

Citations by journals

	2 4 6 8 10 12 14 16 18
Evidence-based Complementary and Alternative Medicine	Evidence-based Complementary and Alternative Medicine, 17, 2.8% Evidence-based Complementary and Alternative Medicine 17 publications, 2.8%
Journal of Biomolecular Structure and Dynamics	Journal of Biomolecular Structure and Dynamics, 14, 2.3% Journal of Biomolecular Structure and Dynamics 14 publications, 2.3%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 13, 2.14% International Journal of Molecular Sciences 13 publications, 2.14%
Nucleic Acids Research	Nucleic Acids Research, 11, 1.81% Nucleic Acids Research 11 publications, 1.81%
Journal of Chemical Information and Modeling	Journal of Chemical Information and Modeling, 10, 1.64% Journal of Chemical Information and Modeling 10 publications, 1.64%
Methods in Molecular Biology	Methods in Molecular Biology, 9, 1.48% Methods in Molecular Biology 9 publications, 1.48%
Briefings in Bioinformatics	Briefings in Bioinformatics, 9, 1.48% Briefings in Bioinformatics 9 publications, 1.48%
Protein Science	Protein Science, 8, 1.32% Protein Science 8 publications, 1.32%
Frontiers in Pharmacology	Frontiers in Pharmacology, 8, 1.32% Frontiers in Pharmacology 8 publications, 1.32%
Molecules	Molecules, 8, 1.32% Molecules 8 publications, 1.32%
Journal of Ethnopharmacology	Journal of Ethnopharmacology, 8, 1.32% Journal of Ethnopharmacology 8 publications, 1.32%
Scientific Reports	Scientific Reports, 7, 1.15% Scientific Reports 7 publications, 1.15%
Bioinformatics	Bioinformatics, 7, 1.15% Bioinformatics 7 publications, 1.15%
BioMed Research International	BioMed Research International, 6, 0.99% BioMed Research International 6 publications, 0.99%
Aging	Aging, 6, 0.99% Aging 6 publications, 0.99%
Medicine (United States)	Medicine (United States), 5, 0.82% Medicine (United States) 5 publications, 0.82%
Pharmaceuticals	Pharmaceuticals, 5, 0.82% Pharmaceuticals 5 publications, 0.82%
Frontiers in Molecular Biosciences	Frontiers in Molecular Biosciences, 5, 0.82% Frontiers in Molecular Biosciences 5 publications, 0.82%
Frontiers in Microbiology	Frontiers in Microbiology, 5, 0.82% Frontiers in Microbiology 5 publications, 0.82%
Nature Communications	Nature Communications, 5, 0.82% Nature Communications 5 publications, 0.82%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 5, 0.82% Computational and Structural Biotechnology Journal 5 publications, 0.82%
International Journal of Biological Macromolecules	International Journal of Biological Macromolecules, 5, 0.82% International Journal of Biological Macromolecules 5 publications, 0.82%
Heliyon	Heliyon, 5, 0.82% Heliyon 5 publications, 0.82%
F1000Research	F1000Research, 4, 0.66% F1000Research 4 publications, 0.66%
Natural Product Communications	Natural Product Communications, 4, 0.66% Natural Product Communications 4 publications, 0.66%
Biomolecules	Biomolecules, 4, 0.66% Biomolecules 4 publications, 0.66%
Frontiers in Genetics	Frontiers in Genetics, 4, 0.66% Frontiers in Genetics 4 publications, 0.66%
BMC Bioinformatics	BMC Bioinformatics, 4, 0.66% BMC Bioinformatics 4 publications, 0.66%
Molecular Diversity	Molecular Diversity, 4, 0.66% Molecular Diversity 4 publications, 0.66%
	2 4 6 8 10 12 14 16 18

Citations by publishers

	20 40 60 80 100 120
Elsevier	Elsevier, 108, 17.76% Elsevier 108 publications, 17.76%
Springer Nature	Springer Nature, 89, 14.64% Springer Nature 89 publications, 14.64%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 52, 8.55% Multidisciplinary Digital Publishing Institute (MDPI) 52 publications, 8.55%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 48, 7.89% Cold Spring Harbor Laboratory 48 publications, 7.89%
Frontiers Media S.A.	Frontiers Media S.A., 40, 6.58% Frontiers Media S.A. 40 publications, 6.58%
Oxford University Press	Oxford University Press, 38, 6.25% Oxford University Press 38 publications, 6.25%
Wiley	Wiley, 31, 5.1% Wiley 31 publications, 5.1%
Hindawi Limited	Hindawi Limited, 30, 4.93% Hindawi Limited 30 publications, 4.93%
Taylor & Francis	Taylor & Francis, 25, 4.11% Taylor & Francis 25 publications, 4.11%
American Chemical Society (ACS)	American Chemical Society (ACS), 23, 3.78% American Chemical Society (ACS) 23 publications, 3.78%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 9, 1.48% Royal Society of Chemistry (RSC) 9 publications, 1.48%
Bentham Science	Bentham Science, 8, 1.32% Bentham Science 8 publications, 1.32%
Impact Journals	Impact Journals, 6, 0.99% Impact Journals 6 publications, 0.99%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 6, 0.99% International Union of Crystallography (IUCr) 6 publications, 0.99%
Wolters Kluwer Health	Wolters Kluwer Health, 6, 0.99% Wolters Kluwer Health 6 publications, 0.99%
SAGE	SAGE, 6, 0.99% SAGE 6 publications, 0.99%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 5, 0.82% Public Library of Science (PLoS) 5 publications, 0.82%
Research Square Platform LLC	Research Square Platform LLC, 5, 0.82% Research Square Platform LLC 5 publications, 0.82%
F1000 Research	F1000 Research, 4, 0.66% F1000 Research 4 publications, 0.66%
IEEE	IEEE, 4, 0.66% IEEE 4 publications, 0.66%
Pleiades Publishing	Pleiades Publishing, 3, 0.49% Pleiades Publishing 3 publications, 0.49%
Dove Medical Press	Dove Medical Press, 3, 0.49% Dove Medical Press 3 publications, 0.49%
PeerJ	PeerJ, 2, 0.33% PeerJ 2 publications, 0.33%
World Scientific	World Scientific, 2, 0.33% World Scientific 2 publications, 0.33%
Walter de Gruyter	Walter de Gruyter, 2, 0.33% Walter de Gruyter 2 publications, 0.33%
American Society for Microbiology	American Society for Microbiology, 2, 0.33% American Society for Microbiology 2 publications, 0.33%
Spandidos Publications	Spandidos Publications, 2, 0.33% Spandidos Publications 2 publications, 0.33%
Canadian Science Publishing	Canadian Science Publishing, 1, 0.16% Canadian Science Publishing 1 publication, 0.16%
The Endocrine Society	The Endocrine Society, 1, 0.16% The Endocrine Society 1 publication, 0.16%
	20 40 60 80 100 120

We do not take into account publications without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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Burley S. K. et al. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive // Methods in Molecular Biology. 2017. pp. 627-641.

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Burley S. K., Berman H. M., KLEYWEGT G. J., Markley J. L., Nakamura H., Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive // Methods in Molecular Biology. 2017. pp. 627-641.

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RIS Copy

TY - GENERIC

DO - 10.1007/978-1-4939-7000-1_26

UR - https://doi.org/10.1007/978-1-4939-7000-1_26

TI - Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

T2 - Methods in Molecular Biology

AU - Burley, Stephen K.

AU - Berman, Helen M.

AU - KLEYWEGT, Gerard J.

AU - Markley, John L.

AU - Nakamura, Haruki

AU - Velankar, Sameer

PY - 2017

DA - 2017/06/01 00:00:00

PB - Springer Nature

SP - 627-641

PMID - 28573592

SN - 1064-3745

SN - 1940-6029

ER -

BibTex

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BibTex Copy

@incollection{2017_Burley,

author = {Stephen K. Burley and Helen M. Berman and Gerard J. KLEYWEGT and John L. Markley and Haruki Nakamura and Sameer Velankar},

title = {Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive},

publisher = {Springer Nature},

year = {2017},

pages = {627--641},

month = {jun}

}

Found error?

Publisher

Springer Nature

Journal

Methods in Molecular Biology

Quartile SCImago

Quartile WOS

—

Impact factor

—

ISSN

10643745 (Print)
19406029 (Electronic)