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Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findabili...

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Autores principales: Young, Jasmine Y, Westbrook, John D, Feng, Zukang, Peisach, Ezra, Persikova, Irina, Sala, Raul, Sen, Sanchayita, Berrisford, John M, Swaminathan, G Jawahar, Oldfield, Thomas J, Gutmanas, Aleksandras, Igarashi, Reiko, Armstrong, David R, Baskaran, Kumaran, Chen, Li, Chen, Minyu, Clark, Alice R, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M S, Hudson, Brian P, Ikegawa, Yasuyo, Kengaku, Yumiko, Lawson, Catherine L, Liang, Yuhe, Mak, Lora, Mukhopadhyay, Abhik, Narayanan, Buvaneswari, Nishiyama, Kayoko, Patwardhan, Ardan, Sahni, Gaurav, Sanz-García, Eduardo, Sato, Junko, Sekharan, Monica R, Shao, Chenghua, Smart, Oliver S, Tan, Lihua, van Ginkel, Glen, Yang, Huanwang, Zhuravleva, Marina A, Markley, John L, Nakamura, Haruki, Kurisu, Genji, Kleywegt, Gerard J, Velankar, Sameer, Berman, Helen M, Burley, Stephen K
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804564/
https://www.ncbi.nlm.nih.gov/pubmed/29688351
http://dx.doi.org/10.1093/database/bay002
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author Young, Jasmine Y
Westbrook, John D
Feng, Zukang
Peisach, Ezra
Persikova, Irina
Sala, Raul
Sen, Sanchayita
Berrisford, John M
Swaminathan, G Jawahar
Oldfield, Thomas J
Gutmanas, Aleksandras
Igarashi, Reiko
Armstrong, David R
Baskaran, Kumaran
Chen, Li
Chen, Minyu
Clark, Alice R
Di Costanzo, Luigi
Dimitropoulos, Dimitris
Gao, Guanghua
Ghosh, Sutapa
Gore, Swanand
Guranovic, Vladimir
Hendrickx, Pieter M S
Hudson, Brian P
Ikegawa, Yasuyo
Kengaku, Yumiko
Lawson, Catherine L
Liang, Yuhe
Mak, Lora
Mukhopadhyay, Abhik
Narayanan, Buvaneswari
Nishiyama, Kayoko
Patwardhan, Ardan
Sahni, Gaurav
Sanz-García, Eduardo
Sato, Junko
Sekharan, Monica R
Shao, Chenghua
Smart, Oliver S
Tan, Lihua
van Ginkel, Glen
Yang, Huanwang
Zhuravleva, Marina A
Markley, John L
Nakamura, Haruki
Kurisu, Genji
Kleywegt, Gerard J
Velankar, Sameer
Berman, Helen M
Burley, Stephen K
author_facet Young, Jasmine Y
Westbrook, John D
Feng, Zukang
Peisach, Ezra
Persikova, Irina
Sala, Raul
Sen, Sanchayita
Berrisford, John M
Swaminathan, G Jawahar
Oldfield, Thomas J
Gutmanas, Aleksandras
Igarashi, Reiko
Armstrong, David R
Baskaran, Kumaran
Chen, Li
Chen, Minyu
Clark, Alice R
Di Costanzo, Luigi
Dimitropoulos, Dimitris
Gao, Guanghua
Ghosh, Sutapa
Gore, Swanand
Guranovic, Vladimir
Hendrickx, Pieter M S
Hudson, Brian P
Ikegawa, Yasuyo
Kengaku, Yumiko
Lawson, Catherine L
Liang, Yuhe
Mak, Lora
Mukhopadhyay, Abhik
Narayanan, Buvaneswari
Nishiyama, Kayoko
Patwardhan, Ardan
Sahni, Gaurav
Sanz-García, Eduardo
Sato, Junko
Sekharan, Monica R
Shao, Chenghua
Smart, Oliver S
Tan, Lihua
van Ginkel, Glen
Yang, Huanwang
Zhuravleva, Marina A
Markley, John L
Nakamura, Haruki
Kurisu, Genji
Kleywegt, Gerard J
Velankar, Sameer
Berman, Helen M
Burley, Stephen K
author_sort Young, Jasmine Y
collection PubMed
description The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/
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spelling pubmed-58045642018-02-23 Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data Young, Jasmine Y Westbrook, John D Feng, Zukang Peisach, Ezra Persikova, Irina Sala, Raul Sen, Sanchayita Berrisford, John M Swaminathan, G Jawahar Oldfield, Thomas J Gutmanas, Aleksandras Igarashi, Reiko Armstrong, David R Baskaran, Kumaran Chen, Li Chen, Minyu Clark, Alice R Di Costanzo, Luigi Dimitropoulos, Dimitris Gao, Guanghua Ghosh, Sutapa Gore, Swanand Guranovic, Vladimir Hendrickx, Pieter M S Hudson, Brian P Ikegawa, Yasuyo Kengaku, Yumiko Lawson, Catherine L Liang, Yuhe Mak, Lora Mukhopadhyay, Abhik Narayanan, Buvaneswari Nishiyama, Kayoko Patwardhan, Ardan Sahni, Gaurav Sanz-García, Eduardo Sato, Junko Sekharan, Monica R Shao, Chenghua Smart, Oliver S Tan, Lihua van Ginkel, Glen Yang, Huanwang Zhuravleva, Marina A Markley, John L Nakamura, Haruki Kurisu, Genji Kleywegt, Gerard J Velankar, Sameer Berman, Helen M Burley, Stephen K Database (Oxford) Original Article The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/ Oxford University Press 2018-02-07 /pmc/articles/PMC5804564/ /pubmed/29688351 http://dx.doi.org/10.1093/database/bay002 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Young, Jasmine Y
Westbrook, John D
Feng, Zukang
Peisach, Ezra
Persikova, Irina
Sala, Raul
Sen, Sanchayita
Berrisford, John M
Swaminathan, G Jawahar
Oldfield, Thomas J
Gutmanas, Aleksandras
Igarashi, Reiko
Armstrong, David R
Baskaran, Kumaran
Chen, Li
Chen, Minyu
Clark, Alice R
Di Costanzo, Luigi
Dimitropoulos, Dimitris
Gao, Guanghua
Ghosh, Sutapa
Gore, Swanand
Guranovic, Vladimir
Hendrickx, Pieter M S
Hudson, Brian P
Ikegawa, Yasuyo
Kengaku, Yumiko
Lawson, Catherine L
Liang, Yuhe
Mak, Lora
Mukhopadhyay, Abhik
Narayanan, Buvaneswari
Nishiyama, Kayoko
Patwardhan, Ardan
Sahni, Gaurav
Sanz-García, Eduardo
Sato, Junko
Sekharan, Monica R
Shao, Chenghua
Smart, Oliver S
Tan, Lihua
van Ginkel, Glen
Yang, Huanwang
Zhuravleva, Marina A
Markley, John L
Nakamura, Haruki
Kurisu, Genji
Kleywegt, Gerard J
Velankar, Sameer
Berman, Helen M
Burley, Stephen K
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
title Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
title_full Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
title_fullStr Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
title_full_unstemmed Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
title_short Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
title_sort worldwide protein data bank biocuration supporting open access to high-quality 3d structural biology data
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804564/
https://www.ncbi.nlm.nih.gov/pubmed/29688351
http://dx.doi.org/10.1093/database/bay002
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