RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
Abstract
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement ofmore »
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- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1899820
- Grant/Contract Number:
- SC0019749
- Resource Type:
- Published Article
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Name: Nucleic Acids Research Journal Volume: 51 Journal Issue: D1; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Burley, Stephen K., Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A., Crichlow, Gregg V., Dalenberg, Kenneth, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W., Ganesan, Sai, Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P., Khokhriakov, Igor, Lawson, Catherine L., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Ben, Westbrook, John D., Whetstone, Shamara, Young, Jasmine Y., Zalevsky, Arthur, and Zardecki, Christine. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. United Kingdom: N. p., 2022.
Web. doi:10.1093/nar/gkac1077.
Burley, Stephen K., Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A., Crichlow, Gregg V., Dalenberg, Kenneth, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W., Ganesan, Sai, Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P., Khokhriakov, Igor, Lawson, Catherine L., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Ben, Westbrook, John D., Whetstone, Shamara, Young, Jasmine Y., Zalevsky, Arthur, & Zardecki, Christine. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. United Kingdom. https://doi.org/10.1093/nar/gkac1077
Burley, Stephen K., Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A., Crichlow, Gregg V., Dalenberg, Kenneth, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W., Ganesan, Sai, Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P., Khokhriakov, Igor, Lawson, Catherine L., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Ben, Westbrook, John D., Whetstone, Shamara, Young, Jasmine Y., Zalevsky, Arthur, and Zardecki, Christine. Thu .
"RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning". United Kingdom. https://doi.org/10.1093/nar/gkac1077.
@article{osti_1899820,
title = {RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning},
author = {Burley, Stephen K. and Bhikadiya, Charmi and Bi, Chunxiao and Bittrich, Sebastian and Chao, Henry and Chen, Li and Craig, Paul A. and Crichlow, Gregg V. and Dalenberg, Kenneth and Duarte, Jose M. and Dutta, Shuchismita and Fayazi, Maryam and Feng, Zukang and Flatt, Justin W. and Ganesan, Sai and Ghosh, Sutapa and Goodsell, David S. and Green, Rachel Kramer and Guranovic, Vladimir and Henry, Jeremy and Hudson, Brian P. and Khokhriakov, Igor and Lawson, Catherine L. and Liang, Yuhe and Lowe, Robert and Peisach, Ezra and Persikova, Irina and Piehl, Dennis W. and Rose, Yana and Sali, Andrej and Segura, Joan and Sekharan, Monica and Shao, Chenghua and Vallat, Brinda and Voigt, Maria and Webb, Ben and Westbrook, John D. and Whetstone, Shamara and Young, Jasmine Y. and Zalevsky, Arthur and Zardecki, Christine},
abstractNote = {Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.},
doi = {10.1093/nar/gkac1077},
journal = {Nucleic Acids Research},
number = D1,
volume = 51,
place = {United Kingdom},
year = {Thu Nov 24 00:00:00 EST 2022},
month = {Thu Nov 24 00:00:00 EST 2022}
}
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Integrating 3D structural information into systems biology
journal, January 2021
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The PDB and the ribosome
journal, January 2021
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Impact of the Protein Data Bank on antineoplastic approvals
journal, May 2020
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ModBase, a database of annotated comparative protein structure models and associated resources
journal, November 2013
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Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
journal, October 2021
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- Protein Science, Vol. 31, Issue 1
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
journal, November 2021
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The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
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Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
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Responsible Data Science
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RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
journal, April 2005
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Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
journal, October 2022
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