RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Stephen K. Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V. Crichlow; Jose M. Duarte; Shuchismita Dutta; Maryam Fayazi; Zukang Feng; Justin W. Flatt; Sai J. Ganesan; David S. Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranovic; Jeremy Henry; Brian P. Hudson; Catherine L. Lawson; Yuhe Liang; Robert Lowe; Ezra Peisach; Irina Persikova; Dennis W. Piehl; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Brinda Vallat; Maria Voigt; John D. Westbrook; Shamara Whetstone; Jasmine Y. Young; Christine Zardecki

doi:https://doi.org/10.1002/pro.4213

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai J. Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Catherine L. Lawson, Yuhe LiangRobert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, John D. Westbrook, Shamara Whetstone, Jasmine Y. Young, Christine Zardecki

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

Original language	American English
Pages (from-to)	187-208
Number of pages	22
Journal	Protein Science
Volume	31
Issue number	1
DOIs	https://doi.org/10.1002/pro.4213
State	Published - Jan 2022

ASJC Scopus subject areas

Biochemistry
Molecular Biology

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Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J. W., Ganesan, S. J., Goodsell, D. S., Ghosh, S., Kramer Green, R., Guranovic, V., Henry, J., Hudson, B. P., Lawson, C. L., ... Zardecki, C. (2022). RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein Science, 31(1), 187-208. https://doi.org/10.1002/pro.4213

@article{7f1eb5bf35354bba8dd7fb740d14c5bb,

title = "RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D",

abstract = "The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.",

author = "Burley, {Stephen K.} and Charmi Bhikadiya and Chunxiao Bi and Sebastian Bittrich and Li Chen and Crichlow, {Gregg V.} and Duarte, {Jose M.} and Shuchismita Dutta and Maryam Fayazi and Zukang Feng and Flatt, {Justin W.} and Ganesan, {Sai J.} and Goodsell, {David S.} and Sutapa Ghosh and {Kramer Green}, Rachel and Vladimir Guranovic and Jeremy Henry and Hudson, {Brian P.} and Lawson, {Catherine L.} and Yuhe Liang and Robert Lowe and Ezra Peisach and Irina Persikova and Piehl, {Dennis W.} and Yana Rose and Andrej Sali and Joan Segura and Monica Sekharan and Chenghua Shao and Brinda Vallat and Maria Voigt and Westbrook, {John D.} and Shamara Whetstone and Young, {Jasmine Y.} and Christine Zardecki",

note = "Funding Information: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; RCSB.org ) is jointly funded by the National Science Foundation, the National Institutes of Health, and the US Department of Energy. Safeguarding and nurturing the PDB archive and providing open access to PDB data are the responsibility of four coordinated RCSB PDB “services,” encompassing data deposition; archive management and access; data exploration; and outreach and education. RCSB PDB, like its wwPDB partners, is committed to the FAIR (Findability, Accessibility, Interoperability, and Reusability) and FACT (Fairness, Accuracy, Confidentiality, and Transparency) Principles emblematic of responsible data stewardship in the modern era. It is no exaggeration to state that the PDB was “walking the walk” decades before people began “talking the talk” regarding these important concepts. 4,5 6 7 Funding Information: Division of Biological Infrastructure, Grant/Award Number: DBI‐1832184; National Cancer Institute, Grant/Award Number: R01GM133198; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; U.S. Department of Energy, Grant/Award Number: DE‐SC0019749; National Science Foundation Funding information Publisher Copyright: {\textcopyright} 2021 The Protein Society.",

year = "2022",

month = jan,

doi = "https://doi.org/10.1002/pro.4213",

language = "American English",

volume = "31",

pages = "187--208",

journal = "Protein science : a publication of the Protein Society",

issn = "0961-8368",

publisher = "Cold Spring Harbor Laboratory Press",

number = "1",

}

Burley, SK, Bhikadiya, C, Bi, C, Bittrich, S, Chen, L, Crichlow, GV, Duarte, JM, Dutta, S, Fayazi, M, Feng, Z, Flatt, JW, Ganesan, SJ, Goodsell, DS, Ghosh, S, Kramer Green, R, Guranovic, V, Henry, J, Hudson, BP, Lawson, CL, Liang, Y, Lowe, R, Peisach, E, Persikova, I, Piehl, DW, Rose, Y, Sali, A, Segura, J, Sekharan, M, Shao, C, Vallat, B, Voigt, M, Westbrook, JD, Whetstone, S, Young, JY & Zardecki, C 2022, 'RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D', Protein Science, vol. 31, no. 1, pp. 187-208. https://doi.org/10.1002/pro.4213

TY - JOUR

T1 - RCSB Protein Data Bank

T2 - Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

AU - Burley, Stephen K.

AU - Bhikadiya, Charmi

AU - Bi, Chunxiao

AU - Bittrich, Sebastian

AU - Chen, Li

AU - Crichlow, Gregg V.

AU - Duarte, Jose M.

AU - Dutta, Shuchismita

AU - Fayazi, Maryam

AU - Feng, Zukang

AU - Flatt, Justin W.

AU - Ganesan, Sai J.

AU - Goodsell, David S.

AU - Ghosh, Sutapa

AU - Kramer Green, Rachel

AU - Guranovic, Vladimir

AU - Henry, Jeremy

AU - Hudson, Brian P.

AU - Lawson, Catherine L.

AU - Liang, Yuhe

AU - Lowe, Robert

AU - Peisach, Ezra

AU - Persikova, Irina

AU - Piehl, Dennis W.

AU - Rose, Yana

AU - Sali, Andrej

AU - Segura, Joan

AU - Sekharan, Monica

AU - Shao, Chenghua

AU - Vallat, Brinda

AU - Voigt, Maria

AU - Westbrook, John D.

AU - Whetstone, Shamara

AU - Young, Jasmine Y.

AU - Zardecki, Christine

N1 - Funding Information: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; RCSB.org ) is jointly funded by the National Science Foundation, the National Institutes of Health, and the US Department of Energy. Safeguarding and nurturing the PDB archive and providing open access to PDB data are the responsibility of four coordinated RCSB PDB “services,” encompassing data deposition; archive management and access; data exploration; and outreach and education. RCSB PDB, like its wwPDB partners, is committed to the FAIR (Findability, Accessibility, Interoperability, and Reusability) and FACT (Fairness, Accuracy, Confidentiality, and Transparency) Principles emblematic of responsible data stewardship in the modern era. It is no exaggeration to state that the PDB was “walking the walk” decades before people began “talking the talk” regarding these important concepts. 4,5 6 7 Funding Information: Division of Biological Infrastructure, Grant/Award Number: DBI‐1832184; National Cancer Institute, Grant/Award Number: R01GM133198; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; U.S. Department of Energy, Grant/Award Number: DE‐SC0019749; National Science Foundation Funding information Publisher Copyright: © 2021 The Protein Society.

PY - 2022/1

Y1 - 2022/1

N2 - The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

AB - The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

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RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Abstract

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