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PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education

The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank i...

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Autores principales: Varadi, Mihaly, Anyango, Stephen, Appasamy, Sri Devan, Armstrong, David, Bage, Marcus, Berrisford, John, Choudhary, Preeti, Bertoni, Damian, Deshpande, Mandar, Leines, Grisell Diaz, Ellaway, Joseph, Evans, Genevieve, Gaborova, Romana, Gupta, Deepti, Gutmanas, Aleksandras, Harrus, Deborah, Kleywegt, Gerard J., Bueno, Weslley Morellato, Nadzirin, Nurul, Nair, Sreenath, Pravda, Lukas, Afonso, Marcelo Querino Lima, Sehnal, David, Tanweer, Ahsan, Tolchard, James, Abrams, Charlotte, Dunlop, Roisin, Velankar, Sameer
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9517934/
https://www.ncbi.nlm.nih.gov/pubmed/36173162
http://dx.doi.org/10.1002/pro.4439
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author Varadi, Mihaly
Anyango, Stephen
Appasamy, Sri Devan
Armstrong, David
Bage, Marcus
Berrisford, John
Choudhary, Preeti
Bertoni, Damian
Deshpande, Mandar
Leines, Grisell Diaz
Ellaway, Joseph
Evans, Genevieve
Gaborova, Romana
Gupta, Deepti
Gutmanas, Aleksandras
Harrus, Deborah
Kleywegt, Gerard J.
Bueno, Weslley Morellato
Nadzirin, Nurul
Nair, Sreenath
Pravda, Lukas
Afonso, Marcelo Querino Lima
Sehnal, David
Tanweer, Ahsan
Tolchard, James
Abrams, Charlotte
Dunlop, Roisin
Velankar, Sameer
author_facet Varadi, Mihaly
Anyango, Stephen
Appasamy, Sri Devan
Armstrong, David
Bage, Marcus
Berrisford, John
Choudhary, Preeti
Bertoni, Damian
Deshpande, Mandar
Leines, Grisell Diaz
Ellaway, Joseph
Evans, Genevieve
Gaborova, Romana
Gupta, Deepti
Gutmanas, Aleksandras
Harrus, Deborah
Kleywegt, Gerard J.
Bueno, Weslley Morellato
Nadzirin, Nurul
Nair, Sreenath
Pravda, Lukas
Afonso, Marcelo Querino Lima
Sehnal, David
Tanweer, Ahsan
Tolchard, James
Abrams, Charlotte
Dunlop, Roisin
Velankar, Sameer
author_sort Varadi, Mihaly
collection PubMed
description The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe‐KB; pdbekb.org), we provide data, data‐access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.
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spelling pubmed-95179342022-10-05 PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education Varadi, Mihaly Anyango, Stephen Appasamy, Sri Devan Armstrong, David Bage, Marcus Berrisford, John Choudhary, Preeti Bertoni, Damian Deshpande, Mandar Leines, Grisell Diaz Ellaway, Joseph Evans, Genevieve Gaborova, Romana Gupta, Deepti Gutmanas, Aleksandras Harrus, Deborah Kleywegt, Gerard J. Bueno, Weslley Morellato Nadzirin, Nurul Nair, Sreenath Pravda, Lukas Afonso, Marcelo Querino Lima Sehnal, David Tanweer, Ahsan Tolchard, James Abrams, Charlotte Dunlop, Roisin Velankar, Sameer Protein Sci Tools for Protein Science The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe‐KB; pdbekb.org), we provide data, data‐access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling. John Wiley & Sons, Inc. 2022-09-28 2022-10 /pmc/articles/PMC9517934/ /pubmed/36173162 http://dx.doi.org/10.1002/pro.4439 Text en © 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Tools for Protein Science
Varadi, Mihaly
Anyango, Stephen
Appasamy, Sri Devan
Armstrong, David
Bage, Marcus
Berrisford, John
Choudhary, Preeti
Bertoni, Damian
Deshpande, Mandar
Leines, Grisell Diaz
Ellaway, Joseph
Evans, Genevieve
Gaborova, Romana
Gupta, Deepti
Gutmanas, Aleksandras
Harrus, Deborah
Kleywegt, Gerard J.
Bueno, Weslley Morellato
Nadzirin, Nurul
Nair, Sreenath
Pravda, Lukas
Afonso, Marcelo Querino Lima
Sehnal, David
Tanweer, Ahsan
Tolchard, James
Abrams, Charlotte
Dunlop, Roisin
Velankar, Sameer
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
title PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
title_full PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
title_fullStr PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
title_full_unstemmed PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
title_short PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
title_sort pdbe and pdbe‐kb: providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
topic Tools for Protein Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9517934/
https://www.ncbi.nlm.nih.gov/pubmed/36173162
http://dx.doi.org/10.1002/pro.4439
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