New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provide...

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Autores principales: Kinjo, Akira R., Bekker, Gert‐Jan, Wako, Hiroshi, Endo, Shigeru, Tsuchiya, Yuko, Sato, Hiromu, Nishi, Hafumi, Kinoshita, Kengo, Suzuki, Hirofumi, Kawabata, Takeshi, Yokochi, Masashi, Iwata, Takeshi, Kobayashi, Naohiro, Fujiwara, Toshimichi, Kurisu, Genji, Nakamura, Haruki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Tools for Protein Science
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734392/
https://www.ncbi.nlm.nih.gov/pubmed/28815765
http://dx.doi.org/10.1002/pro.3273
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author Kinjo, Akira R.
Bekker, Gert‐Jan
Wako, Hiroshi
Endo, Shigeru
Tsuchiya, Yuko
Sato, Hiromu
Nishi, Hafumi
Kinoshita, Kengo
Suzuki, Hirofumi
Kawabata, Takeshi
Yokochi, Masashi
Iwata, Takeshi
Kobayashi, Naohiro
Fujiwara, Toshimichi
Kurisu, Genji
Nakamura, Haruki
author_facet Kinjo, Akira R.
Bekker, Gert‐Jan
Wako, Hiroshi
Endo, Shigeru
Tsuchiya, Yuko
Sato, Hiromu
Nishi, Hafumi
Kinoshita, Kengo
Suzuki, Hirofumi
Kawabata, Takeshi
Yokochi, Masashi
Iwata, Takeshi
Kobayashi, Naohiro
Fujiwara, Toshimichi
Kurisu, Genji
Nakamura, Haruki
author_sort Kinjo, Akira R.
collection PubMed
description The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode‐Elastic server for normal mode analysis, a virtual reality system for the eF‐site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.
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spelling pubmed-57343922017-12-21 New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj) Kinjo, Akira R. Bekker, Gert‐Jan Wako, Hiroshi Endo, Shigeru Tsuchiya, Yuko Sato, Hiromu Nishi, Hafumi Kinoshita, Kengo Suzuki, Hirofumi Kawabata, Takeshi Yokochi, Masashi Iwata, Takeshi Kobayashi, Naohiro Fujiwara, Toshimichi Kurisu, Genji Nakamura, Haruki Protein Sci Tools for Protein Science The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode‐Elastic server for normal mode analysis, a virtual reality system for the eF‐site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches. John Wiley and Sons Inc. 2017-09-18 2018-01 /pmc/articles/PMC5734392/ /pubmed/28815765 http://dx.doi.org/10.1002/pro.3273 Text en © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs (http://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Tools for Protein Science
Kinjo, Akira R.
Bekker, Gert‐Jan
Wako, Hiroshi
Endo, Shigeru
Tsuchiya, Yuko
Sato, Hiromu
Nishi, Hafumi
Kinoshita, Kengo
Suzuki, Hirofumi
Kawabata, Takeshi
Yokochi, Masashi
Iwata, Takeshi
Kobayashi, Naohiro
Fujiwara, Toshimichi
Kurisu, Genji
Nakamura, Haruki
New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
title New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
title_full New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
title_fullStr New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
title_full_unstemmed New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
title_short New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
title_sort new tools and functions in data‐out activities at protein data bank japan (pdbj)
topic Tools for Protein Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734392/
https://www.ncbi.nlm.nih.gov/pubmed/28815765
http://dx.doi.org/10.1002/pro.3273
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