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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

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,...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825554/
https://www.ncbi.nlm.nih.gov/pubmed/36420884
http://dx.doi.org/10.1093/nar/gkac1077
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author 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
author_facet 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
author_sort Burley, Stephen K
collection PubMed
description 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.
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spelling pubmed-98255542023-01-10 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 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 Nucleic Acids Res Database Issue 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. Oxford University Press 2022-11-24 /pmc/articles/PMC9825554/ /pubmed/36420884 http://dx.doi.org/10.1093/nar/gkac1077 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
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
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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_short 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
title_sort 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
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825554/
https://www.ncbi.nlm.nih.gov/pubmed/36420884
http://dx.doi.org/10.1093/nar/gkac1077
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