Cargando…
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,...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1784866657859010560 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9825554 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT burleystephenk rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT bhikadiyacharmi rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT bichunxiao rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT bittrichsebastian rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT chaohenry rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT chenli rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT craigpaula rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT crichlowgreggv rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT dalenbergkenneth rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT duartejosem rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT duttashuchismita rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT fayazimaryam rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT fengzukang rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT flattjustinw rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT ganesansai rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT ghoshsutapa rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT goodselldavids rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT greenrachelkramer rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT guranovicvladimir rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT henryjeremy rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT hudsonbrianp rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT khokhriakovigor rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT lawsoncatherinel rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT liangyuhe rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT lowerobert rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT peisachezra rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT persikovairina rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT piehldennisw rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT roseyana rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT saliandrej rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT segurajoan rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT sekharanmonica rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT shaochenghua rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT vallatbrinda rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT voigtmaria rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT webbben rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT westbrookjohnd rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT whetstoneshamara rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT youngjasminey rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT zalevskyarthur rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning AT zardeckichristine rcsbproteindatabankrcsborgdeliveryofexperimentallydeterminedpdbstructuresalongsideonemillioncomputedstructuremodelsofproteinsfromartificialintelligencemachinelearning |