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Protein Data Bank Japan

Recommended

General Information

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

Homepage http://www.pdbj.org/

Countries that developed this resource Japan

Created in 2011

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

COVID-19

In the following recommendations:

How to cite this record FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Oct 19 2021 12:51 p.m.

Record updated: April 20, 2021, 9:53 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.rs2815' by 'The FAIRsharing Team' at 09:53, 20 Apr 2021 (approved):

	'licences' has been modified:
		Before:
			Attribution required||Data
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
		After:
			PDBJ Attribution required|https://pdbj.org/info/terms-conditions|Data
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
		Added:
			PDBJ Attribution required|https://pdbj.org/info/terms-conditions|Data
		Removed:
			Attribution required||Data

Edits to 'https://fairsharing.org/FAIRsharing.rs2815' by 'The FAIRsharing Team' at 11:02, 23 Feb 2021 (approved):

	'onto_domains' has been modified:
		Before:
			Function analysis
			protein
			structure
		After:
			Function analysis
			Structure
			protein
			structure
		Added:
			Structure
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Edits to 'https://fairsharing.org/FAIRsharing.rs2815' by 'The FAIRsharing Team' at 09:07, 23 Apr 2020 (approved):

	'organizations' has been modified:
		Before:
			Osaka University, Japan|http://www.osaka-u.ac.jp/en|Maintains
		After:
			Osaka University, Japan|http://www.osaka-u.ac.jp/en|Maintains
			Database Integration Coordination Program from the National Bioscience Database Center, Tokyo, Japan|https://biosciencedbc.jp/en/funding/program/dicp/|Funds
			Platform Project for Supporting in Drug Discovery and Life Science Research, Tokyo, Japan|https://www.amed.go.jp/en/index.html|Funds
			Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (JST), Tokyo, Japan|https://www.jst.go.jp/nbdc/bird/index_e.html|Funds
			Japan Society for the Promotion of Science (JSPS), Tokyo, Japan|https://www.jsps.go.jp/index.html|Funds
		Added:
			Database Integration Coordination Program from the National Bioscience Database Center, Tokyo, Japan|https://biosciencedbc.jp/en/funding/program/dicp/|Funds
			Platform Project for Supporting in Drug Discovery and Life Science Research, Tokyo, Japan|https://www.amed.go.jp/en/index.html|Funds
			Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (JST), Tokyo, Japan|https://www.jst.go.jp/nbdc/bird/index_e.html|Funds
			Japan Society for the Promotion of Science (JSPS), Tokyo, Japan|https://www.jsps.go.jp/index.html|Funds
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			COVID-19
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			COVID-19
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	'onto_disciplines' has been modified:
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			Life Science
			Proteomics
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			Epidemiology
			Life Science
			Proteomics
			Virology
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			Epidemiology
			Virology
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			26440078
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			26440078
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	'miriam_id' has been modified:
		Before: None
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	'publications' has been modified:
		Before:
			Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.|Kinjo AR., Suzuki H., Yamashita R., Ikegawa Y., Kudou T., Igarashi R., Kengaku Y., Cho H., Standley DM., Nakagawa A., Nakamura H., |Nucleic Acids Res.|2012
		After:
			Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.|Kinjo AR., Suzuki H., Yamashita R., Ikegawa Y., Kudou T., Igarashi R., Kengaku Y., Cho H., Standley DM., Nakagawa A., Nakamura H., |Nucleic Acids Res.|2012
			[Development of PDBj: Advanced database for protein structures].|Nakamura H,Ito N,Kusunoki M|Tanpakushitsu Kakusan Koso|2002
			PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.|Kinjo AR,Yamashita R,Nakamura H|Database (Oxford)|2010
			Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr.|Nakamura H|J Comput Aided Mol Des|2011
			Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.|Kinjo AR,Bekker GJ,Suzuki H,Tsuchiya Y,Kawabata T,Ikegawa Y,Nakamura H|Nucleic Acids Res|2016
			New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).|Kinjo AR,Bekker GJ,Wako H,Endo S,Tsuchiya Y,Sato H,Nishi H,Kinoshita K,Suzuki H,Kawabata T,Yokochi M,Iwata T,Kobayashi N,Fujiwara T,Kurisu G,Nakamura H|Protein Sci|2017
		Added:
			[Development of PDBj: Advanced database for protein structures].|Nakamura H,Ito N,Kusunoki M|Tanpakushitsu Kakusan Koso|2002
			PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.|Kinjo AR,Yamashita R,Nakamura H|Database (Oxford)|2010
			Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr.|Nakamura H|J Comput Aided Mol Des|2011
			Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.|Kinjo AR,Bekker GJ,Suzuki H,Tsuchiya Y,Kawabata T,Ikegawa Y,Nakamura H|Nucleic Acids Res|2016
			New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).|Kinjo AR,Bekker GJ,Wako H,Endo S,Tsuchiya Y,Sato H,Nishi H,Kinoshita K,Suzuki H,Kawabata T,Yokochi M,Iwata T,Kobayashi N,Fujiwara T,Kurisu G,Nakamura H|Protein Sci|2017
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.rs2815' by 'The FAIRsharing Team' at 22:40, 20 Aug 2016 (approved):

	'contactName' has been modified:
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		After:
			Haruki Nakamura
		Added:
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In Collections

COVID-19 Resources

RDA Covid-19 WG Resources

Support

General

FAQ	http://pdbj.org/#!help?PID=5
contact form	http://pdbj.org/#!contact?tab=PDBjmaster
help	http://pdbj.org/help/
twitter	@PDBj_en

Additional Information

Contact

Haruki Nakamura ORCID

Tools

ASH	http://sysimm.ifrec.osaka-u.ac.jp/ash_service/
Yorodumi	http://pdbj.org/emnavi/viewtop.php
MAFFTash	http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/	4.1
NMR Tool Box	http://bmrbdep.pdbj.org/en/nmrtoolbox/
Pairwise gmfit	http://pdbj.org/gmfit/
CRNPRED	http://pdbj.org/crnpred/
Spanner	http://pdbj.org/spanner/
SFAS	https://sysimm.ifrec.osaka-u.ac.jp/pipeline7/
HOMCOS	http://homcos.pdbj.org/?LANG=en

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Access

Download	http://pdbj.org/#!showBlogPost?PID=8
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search	http://pdbj.org/#!mine

Publications

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

Kinjo AR., Suzuki H., Yamashita R., Ikegawa Y., Kudou T., Igarashi R., Kengaku Y., Cho H., Standley DM., Nakagawa A., Nakamura H.,
Nucleic Acids Res. 2012