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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

Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interfa...

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Autores principales: Bekker, Gert‐Jan, Yokochi, Masashi, Suzuki, Hirofumi, Ikegawa, Yasuyo, Iwata, Takeshi, Kudou, Takahiro, Yura, Kei, Fujiwara, Toshimichi, Kawabata, Takeshi, Kurisu, Genji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8740847/
https://www.ncbi.nlm.nih.gov/pubmed/34664328
http://dx.doi.org/10.1002/pro.4211
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author Bekker, Gert‐Jan
Yokochi, Masashi
Suzuki, Hirofumi
Ikegawa, Yasuyo
Iwata, Takeshi
Kudou, Takahiro
Yura, Kei
Fujiwara, Toshimichi
Kawabata, Takeshi
Kurisu, Genji
author_facet Bekker, Gert‐Jan
Yokochi, Masashi
Suzuki, Hirofumi
Ikegawa, Yasuyo
Iwata, Takeshi
Kudou, Takahiro
Yura, Kei
Fujiwara, Toshimichi
Kawabata, Takeshi
Kurisu, Genji
author_sort Bekker, Gert‐Jan
collection PubMed
description Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers.
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spelling pubmed-87408472022-01-12 Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data Bekker, Gert‐Jan Yokochi, Masashi Suzuki, Hirofumi Ikegawa, Yasuyo Iwata, Takeshi Kudou, Takahiro Yura, Kei Fujiwara, Toshimichi Kawabata, Takeshi Kurisu, Genji Protein Sci Tools for Protein Science Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers. John Wiley & Sons, Inc. 2021-10-27 2022-01 /pmc/articles/PMC8740847/ /pubmed/34664328 http://dx.doi.org/10.1002/pro.4211 Text en © 2021 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
Bekker, Gert‐Jan
Yokochi, Masashi
Suzuki, Hirofumi
Ikegawa, Yasuyo
Iwata, Takeshi
Kudou, Takahiro
Yura, Kei
Fujiwara, Toshimichi
Kawabata, Takeshi
Kurisu, Genji
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
title Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
title_full Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
title_fullStr Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
title_full_unstemmed Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
title_short Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
title_sort protein data bank japan: celebrating our 20th anniversary during a global pandemic as the asian hub of three dimensional macromolecular structural data
topic Tools for Protein Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8740847/
https://www.ncbi.nlm.nih.gov/pubmed/34664328
http://dx.doi.org/10.1002/pro.4211
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