Analysis of impact metrics for the Protein Data Bank
Abstract
Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules. The archive currently holds >140,000 structures (>1 billion atoms). These structures are the molecules of life found in all organisms. Knowing the 3D structure of a biological macromolecule is essential for understanding the molecule’s function, providing insights in health and disease, food and energy production, and other topics of concern to prosperity and sustainability. PDB data are freely and publicly available, without restrictions on usage. Through bibliometric and usage studies, we sought to determine the impact of the PDB across disciplines and demographics. Our analysis shows that even though research areas such as molecular biology and biochemistry account for the most usage, other fields are increasingly using PDB resources. PDB usage is seen across 150 disciplines in applied sciences, humanities, and social sciences. Data are also re-used and integrated with >400 resources. Our study identifies trends in PDB usage and documents its utility across research disciplines.
- Authors:
-
- Rutgers Univ., Piscataway, NJ (United States)
- Rutgers Univ., Piscataway, NJ (United States); Univ. of California San Diego, La Jolla, CA (United States)
- Publication Date:
- Research Org.:
- Rutgers Univ., Piscataway, NJ (United States)
- Sponsoring Org.:
- USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)
- OSTI Identifier:
- 1624555
- Grant/Contract Number:
- NSF-DBI 1338415
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Data
- Additional Journal Information:
- Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2052-4463
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; science and technology; databases; literature mining; publishing; structural biology
Citation Formats
Markosian, Christopher, Di Costanzo, Luigi, Sekharan, Monica, Shao, Chenghua, Burley, Stephen K., and Zardecki, Christine. Analysis of impact metrics for the Protein Data Bank. United States: N. p., 2018.
Web. doi:10.1038/sdata.2018.212.
Markosian, Christopher, Di Costanzo, Luigi, Sekharan, Monica, Shao, Chenghua, Burley, Stephen K., & Zardecki, Christine. Analysis of impact metrics for the Protein Data Bank. United States. https://doi.org/10.1038/sdata.2018.212
Markosian, Christopher, Di Costanzo, Luigi, Sekharan, Monica, Shao, Chenghua, Burley, Stephen K., and Zardecki, Christine. Tue .
"Analysis of impact metrics for the Protein Data Bank". United States. https://doi.org/10.1038/sdata.2018.212. https://www.osti.gov/servlets/purl/1624555.
@article{osti_1624555,
title = {Analysis of impact metrics for the Protein Data Bank},
author = {Markosian, Christopher and Di Costanzo, Luigi and Sekharan, Monica and Shao, Chenghua and Burley, Stephen K. and Zardecki, Christine},
abstractNote = {Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules. The archive currently holds >140,000 structures (>1 billion atoms). These structures are the molecules of life found in all organisms. Knowing the 3D structure of a biological macromolecule is essential for understanding the molecule’s function, providing insights in health and disease, food and energy production, and other topics of concern to prosperity and sustainability. PDB data are freely and publicly available, without restrictions on usage. Through bibliometric and usage studies, we sought to determine the impact of the PDB across disciplines and demographics. Our analysis shows that even though research areas such as molecular biology and biochemistry account for the most usage, other fields are increasingly using PDB resources. PDB usage is seen across 150 disciplines in applied sciences, humanities, and social sciences. Data are also re-used and integrated with >400 resources. Our study identifies trends in PDB usage and documents its utility across research disciplines.},
doi = {10.1038/sdata.2018.212},
journal = {Scientific Data},
number = 1,
volume = 5,
place = {United States},
year = {Tue Oct 16 00:00:00 EDT 2018},
month = {Tue Oct 16 00:00:00 EDT 2018}
}
Figures / Tables:
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STRING v10: protein–protein interaction networks, integrated over the tree of life
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The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease
journal, October 2014
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IMGT®, the international ImMunoGeneTics information system® 25 years on
journal, November 2014
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ArrayExpress update—simplifying data submissions
journal, October 2014
- Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria
- Nucleic Acids Research, Vol. 43, Issue D1
Rfam 12.0: updates to the RNA families database
journal, November 2014
- Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex
- Nucleic Acids Research, Vol. 43, Issue D1
Genenames.org: the HGNC resources in 2015
journal, October 2014
- Gray, Kristian A.; Yates, Bethan; Seal, Ruth L.
- Nucleic Acids Research, Vol. 43, Issue D1
COSMIC: exploring the world's knowledge of somatic mutations in human cancer
journal, October 2014
- Forbes, Simon A.; Beare, David; Gunasekaran, Prasad
- Nucleic Acids Research, Vol. 43, Issue D1
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases
journal, December 2014
- Giraldo-Calderón, Gloria I.; Emrich, Scott J.; MacCallum, Robert M.
- Nucleic Acids Research, Vol. 43, Issue D1
Cancer3D: understanding cancer mutations through protein structures
journal, November 2014
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- Nucleic Acids Research, Vol. 43, Issue D1
CDD: NCBI's conserved domain database
journal, November 2014
- Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.
- Nucleic Acids Research, Vol. 43, Issue D1
The immune epitope database (IEDB) 3.0
journal, October 2014
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- Nucleic Acids Research, Vol. 43, Issue D1
SMART: recent updates, new developments and status in 2015
journal, October 2014
- Letunic, Ivica; Doerks, Tobias; Bork, Peer
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ChEBI in 2016: Improved services and an expanding collection of metabolites
journal, October 2015
- Hastings, Janna; Owen, Gareth; Dekker, Adriano
- Nucleic Acids Research, Vol. 44, Issue D1
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB
journal, October 2015
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