Analysis of impact metrics for the Protein Data Bank

Markosian, Christopher; Di Costanzo, Luigi; Sekharan, Monica; Shao, Chenghua; Burley, Stephen K.; Zardecki, Christine

doi:10.1038/sdata.2018.212

Title: 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:

Markosian, Christopher ^[1]; Di Costanzo, Luigi ^[1]; Sekharan, Monica ^[1]; Shao, Chenghua ^[1]; Burley, Stephen K. ^[2]; Zardecki, Christine ^[1]

Rutgers Univ., Piscataway, NJ (United States)
Rutgers Univ., Piscataway, NJ (United States); Univ. of California San Diego, La Jolla, CA (United States)

Publication Date:: Tue Oct 16 00:00:00 EDT 2018

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.

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                    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

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                    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.

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@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}

}

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Figures / Tables:

Figure 1: Number of publications for the top-assigned Web of Science Journal Subject Category for all documents (2000–2016) citing the inaugural Berman et al. (2000) reference. Biochemistry Molecular Biology is the largest category (6,735 publications), followed by Biophysics (2,872), Biochemical Research Methods (2,161), Computer Science Interdisciplinary Applications (1,852), Chemistry Medicinalmore »

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