Protein Data Bank in Europe

Abbreviation:PDBe

Recommended

General Information

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.

Homepage http://www.pdbe.org

Countries that developed this resource European Union , United Kingdom

Created in 1996

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: PDBe; Protein Data Bank in Europe; DOI: https://doi.org/10.25504/FAIRsharing.26ek1v; Last edited: Jan. 9, 2019, 1:15 p.m.; Last accessed: Aug 22 2019 3:29 a.m.

This record is maintained by PDBe

Record updated: Jan. 9, 2019, 1:15 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 13:13, 09 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			European Union (EU)|http://europa.eu/index_en.htm|Funds
			Medical Research Council (MRC), London, UK|http://www.emouseatlas.org/emap/home.html|Funds
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA|http://www.nigms.nih.gov|Funds
		After:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			European Union (EU)|http://europa.eu/index_en.htm|Funds
			Medical Research Council (MRC), London, UK|http://www.emouseatlas.org/emap/home.html|Funds
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA|http://www.nigms.nih.gov|Funds
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains

	'supportLinks' has been modified:
		Before:
			contact form|http://www.ebi.ac.uk/support/pdbe
			online documentation|http://www.ebi.ac.uk/pdbe/documentation
			tess training|https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank
			tess training|https://tess.elixir-europe.org/materials/pdbe-quick-tour
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures
			tess training|https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry
			training|http://www.ebi.ac.uk/pdbe/training
			twitter|@PDBeurope
		After:
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-quick-tour
			contact form|http://www.ebi.ac.uk/support/pdbe
			online documentation|http://www.ebi.ac.uk/pdbe/documentation
			online documentation|http://www.ebi.ac.uk/pdbe/deposition
			online documentation|https://www.ebi.ac.uk/pdbe/about/news
			training|https://www.ebi.ac.uk/pdbe/training
			twitter|@PDBeurope
		Added:
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank
			TeSS training|https://tess.elixir-europe.org/materials/pdbe-quick-tour
			online documentation|http://www.ebi.ac.uk/pdbe/deposition
			online documentation|https://www.ebi.ac.uk/pdbe/about/news
			training|https://www.ebi.ac.uk/pdbe/training
		Removed:
			tess training|https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank
			tess training|https://tess.elixir-europe.org/materials/pdbe-quick-tour
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures
			tess training|https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry
			training|http://www.ebi.ac.uk/pdbe/training

	'description' has been modified:
		Before: The Protein Data Bank in Europe is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.
		After: The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.

	'licences' has been modified:
		Before:
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
		After:
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
			wwPDB Charter|https://www.wwpdb.org/about/agreement|Data
			PDBe Data Access Statement|https://www.ebi.ac.uk/pdbe/about/access|Data
		Added:
			wwPDB Charter|https://www.wwpdb.org/about/agreement|Data
			PDBe Data Access Statement|https://www.ebi.ac.uk/pdbe/about/access|Data
		Removed:

	'dataProcesses' has been modified:
		Before:
			Download
			Manual curation
			OneDep: Data Deposition Portal
			search by sequence
			PDBeFold- Search by structure
			Search
		After:
			Download
			OneDep: Data Deposition Portal
			search by sequence
			PDBeFold- Search by structure
			Search
		Added:
		Removed:
			Manual curation

	'contact' has been modified:
		Before: None
		After: PDBe Helpdesk

	'miriam_id' has been modified:
		Before: 
		After: MIR:00100037

	'publications' has been modified:
		Before:
			PDBe: Protein Data Bank in Europe.|Velankar S., Alhroub Y., Best C., Caboche S., Conroy MJ., Dana JM., Fernandez Montecelo MA., van Ginkel G., Golovin A., Gore SP., Gutmanas A., Haslam P., Hendrickx PM., Heuson E., Hirshberg M., John M., Lagerstedt I., Mir S., Newman LE., Oldfield TJ., Patwardhan A., Rinaldi L., Sahni G., Sanz-Garca E., Sen S., Slowley R., Suarez-Uruena A., Swaminathan GJ., Symmons MF., Vranken WF., Wainwright M., Kleywegt GJ., |Nucleic Acids Res.|2012
			PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.|Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-Garca E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ.|Nucleic Acids Res.|2016
			The archiving and dissemination of biological structure data|    Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar|Current Opinion in Structural Biology|2016
		After:
			PDBe: Protein Data Bank in Europe.|Velankar S., Alhroub Y., Best C., Caboche S., Conroy MJ., Dana JM., Fernandez Montecelo MA., van Ginkel G., Golovin A., Gore SP., Gutmanas A., Haslam P., Hendrickx PM., Heuson E., Hirshberg M., John M., Lagerstedt I., Mir S., Newman LE., Oldfield TJ., Patwardhan A., Rinaldi L., Sahni G., Sanz-Garca E., Sen S., Slowley R., Suarez-Uruena A., Swaminathan GJ., Symmons MF., Vranken WF., Wainwright M., Kleywegt GJ., |Nucleic Acids Res.|2012
			PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.|Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-Garca E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ.|Nucleic Acids Res.|2016
			The archiving and dissemination of biological structure data|    Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar|Current Opinion in Structural Biology|2016
			PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.|Mir S,Alhroub Y,Anyango S,Armstrong DR,Berrisford JM,Clark AR,Conroy MJ,Dana JM,Deshpande M,Gupta D,Gutmanas A,Haslam P,Mak L,Mukhopadhyay A,Nadzirin N,Paysan-Lafosse T,Sehnal D,Sen S,Smart OS,Varadi M,Kleywegt GJ,Velankar S|Nucleic Acids Res|2017
		Added:
			PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.|Mir S,Alhroub Y,Anyango S,Armstrong DR,Berrisford JM,Clark AR,Conroy MJ,Dana JM,Deshpande M,Gupta D,Gutmanas A,Haslam P,Mak L,Mukhopadhyay A,Nadzirin N,Paysan-Lafosse T,Sehnal D,Sen S,Smart OS,Varadi M,Kleywegt GJ,Velankar S|Nucleic Acids Res|2017
		Removed:

	'tools' has been modified:
		Before:
			EMDB||http://www.ebi.ac.uk/pdbe/emdb
			PDBePISA||http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
			wwPDB Validation Service||http://validate.wwpdb.org
		After:
			EMDB||http://www.ebi.ac.uk/pdbe/emdb
			PDBePISA||http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
			wwPDB Validation Service||http://validate.wwpdb.org
			Full PDBe Tools List||https://www.ebi.ac.uk/pdbe/services
		Added:
			Full PDBe Tools List||https://www.ebi.ac.uk/pdbe/services
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 14:01, 07 Aug 2018 (approved):

	'supportLinks' has been modified:
		Before:
			contact form|http://www.ebi.ac.uk/support/pdbe
			online documentation|http://www.ebi.ac.uk/pdbe/documentation
			training|http://www.ebi.ac.uk/pdbe/training
			twitter|@PDBeurope
		After:
			contact form|http://www.ebi.ac.uk/support/pdbe
			online documentation|http://www.ebi.ac.uk/pdbe/documentation
			tess training|https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank
			tess training|https://tess.elixir-europe.org/materials/pdbe-quick-tour
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures
			tess training|https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry
			training|http://www.ebi.ac.uk/pdbe/training
			twitter|@PDBeurope
		Added:
			tess training|https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank
			tess training|https://tess.elixir-europe.org/materials/pdbe-quick-tour
			tess training|https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures
			tess training|https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 09:58, 07 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			European Union (EU)|http://ec.europa.eu/chafea/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			US National Institutes of Health (NIH)|https://www.nih.gov/|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			Medical Research Council (MRC), London, United Kingdom|http://www.mrc.ac.uk|Funds
		After:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			European Union (EU)|http://ec.europa.eu/chafea/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			US National Institutes of Health (NIH)|https://www.nih.gov/|Funds
			Medical Research Council (MRC), London, United Kingdom|http://www.mrc.ac.uk|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			US National Institute of General Medical Sciences, (NIGMS)|http://www.nigms.nih.gov|Funds
			US National Science Foundation (NSF)|http://www.nsf.gov/|Funds
		Added:
			US National Institute of General Medical Sciences, (NIGMS)|http://www.nigms.nih.gov|Funds
			US National Science Foundation (NSF)|http://www.nsf.gov/|Funds
		Removed:

	'grants' has been modified:
		Before:
			088944
			104948
			226073
			284209
			BB/E007511/1
			BB/G022577/1
			BB/J007471/1
			BB/K016970/1
			BB/M011674/1
			BB/M013146/1
			GM079429
			MR/L007835/1
			R01GM079429-01A1
		After:
			088944
			104948
			1RO1 GM079429-01A1
			226073
			284209
			675858
			BB/E007511/1
			BB/G022577/1
			BB/J007471/1
			BB/K016970/1
			BB/K020013/1
			BB/M011674/1
			BB/M011674/1
			BB/M013146/1
			BB/M020347/1
			BB/M020428/1
			DBI-1338415
			GM079429
			MR/L007835/1
			R01GM079429-01A1
		Added:
			1RO1 GM079429-01A1
			675858
			BB/K020013/1
			BB/M020347/1
			BB/M020428/1
			DBI-1338415
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 09:48, 07 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			European Union (EU)|http://ec.europa.eu/chafea/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			US National Institutes of Health (NIH)|https://www.nih.gov/|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
		After:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			European Union (EU)|http://ec.europa.eu/chafea/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			US National Institutes of Health (NIH)|https://www.nih.gov/|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			Medical Research Council (MRC), London, United Kingdom|http://www.mrc.ac.uk|Funds
		Added:
			Medical Research Council (MRC), London, United Kingdom|http://www.mrc.ac.uk|Funds
		Removed:

	'grants' has been modified:
		Before:
			088944
			104948
			226073
			BB/E007511/1
			BB/G022577/1
			BB/J007471/1
			BB/K016970/1
			BB/M011674/1
			BB/M013146/1
			R01GM079429-01A1
		After:
			088944
			104948
			226073
			284209
			BB/E007511/1
			BB/G022577/1
			BB/J007471/1
			BB/K016970/1
			BB/M011674/1
			BB/M013146/1
			GM079429
			MR/L007835/1
			R01GM079429-01A1
		Added:
			284209
			GM079429
			MR/L007835/1
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 09:31, 07 Aug 2018 (approved):

	'grants' has been modified:
		Before:
			088944
			226073
			BB/E007511/1
			BB/G022577/1
			R01GM079429-01A1
		After:
			088944
			104948
			226073
			BB/E007511/1
			BB/G022577/1
			BB/J007471/1
			BB/K016970/1
			BB/M011674/1
			BB/M013146/1
			R01GM079429-01A1
		Added:
			104948
			BB/J007471/1
			BB/K016970/1
			BB/M011674/1
			BB/M013146/1
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 09:26, 07 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
		After:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			West-Life|http://about.west-life.eu/update/network/west-life/west-life|Funds
			Central European Institute of Technology|https://www.ceitec.eu/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Union (EU)|http://ec.europa.eu/chafea/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			US National Institutes of Health (NIH)|https://www.nih.gov/|Funds
		Added:
			European Union (EU)|http://ec.europa.eu/chafea/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			US National Institutes of Health (NIH)|https://www.nih.gov/|Funds
		Removed:

	'grants' has been modified:
		Before:
		After:
			088944
			226073
			BB/E007511/1
			BB/G022577/1
			R01GM079429-01A1
		Added:
			088944
			226073
			BB/E007511/1
			BB/G022577/1
			R01GM079429-01A1
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'The FAIRsharing Team' at 09:20, 07 Aug 2018 (approved):

	'miriam_id' has been modified:
		Before: None
		After: 

	'contact' has been modified:
		Before: None
		After: None

	'tools' has been modified:
		Before:
			OneDep: Data Deposition Portal||http://deposit-pdbe.wwpdb.org/
			search by sequence||http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/
			PDBeFold- Search by structure||http://www.ebi.ac.uk/msd-srv/ssm/
			EMDB||http://www.ebi.ac.uk/pdbe/emdb
			Search||http://www.pdbe.org
			EMPIAR||http://www.ebi.ac.uk/pdbe/empiar
			wwPDB Validation Service||http://validate.wwpdb.org
		After:
			EMDB||http://www.ebi.ac.uk/pdbe/emdb
			PDBePISA||http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
			wwPDB Validation Service||http://validate.wwpdb.org
		Added:
			PDBePISA||http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
		Removed:
			OneDep: Data Deposition Portal||http://deposit-pdbe.wwpdb.org/
			search by sequence||http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/
			PDBeFold- Search by structure||http://www.ebi.ac.uk/msd-srv/ssm/
			Search||http://www.pdbe.org
			EMPIAR||http://www.ebi.ac.uk/pdbe/empiar

	'dataProcesses' has been modified:
		Before:
			Download
			Manual curation
		After:
			Download
			Manual curation
			OneDep: Data Deposition Portal
			search by sequence
			PDBeFold- Search by structure
			Search
		Added:
			OneDep: Data Deposition Portal
			search by sequence
			PDBeFold- Search by structure
			Search
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'PDBe' at 14:34, 22 Mar 2017 (approved):

	'miriam_url' has been modified:
		Before: None
		After: http://www.ebi.ac.uk/miriam/main/resources/MIR:00100037 Tools have changed:  Previous values: Deposit search by sequence PDBeFold- Search by structure EMDB Search EMPIAR New values:  OneDep: Data Deposition Portal search by sequence PDBeFold- Search by structure EMDB Search EMPIAR wwPDB Validation Service Organisations have changed:  Previous values: EMBL Swiss Institute of Bioinformatics (SIB)|Switzerland The Wellcome Trust|UK New values:  EMBL Swiss Institute of Bioinformatics (SIB)|Switzerland The Wellcome Trust|UK CEITEC|Masaryk University|Czech Republic West-Life

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'PDBe' at 14:21, 21 Mar 2017 (approved):

	'miriam_url' has been modified:
		Before: None
		After: http://www.ebi.ac.uk/miriam/main/resources/MIR:00100037 Tools have changed:  Previous values: Deposit search by sequence PDBeFold- Search by structure EMDB Search EMPIAR New values:  OneDep: Data Deposition Portal search by sequence PDBeFold- Search by structure EMDB Search EMPIAR wwPDB Validation Service Organisations have changed:  Previous values: EMBL Swiss Institute of Bioinformatics (SIB)|Switzerland The Wellcome Trust|UK New values:  EMBL Swiss Institute of Bioinformatics (SIB)|Switzerland The Wellcome Trust|UK CEITEC|Masaryk University|Czech Republic West-Life

Edits to 'https://fairsharing.org/FAIRsharing.26ek1v' by 'PDBe' at 19:40, 01 Aug 2016 (approved):

	'description' has been modified:
		Before: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
		After: The Protein Data Bank in Europe is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.

In Collections

ELIXIR Core Data Resources and Deposition Databases

Support

General

contact form	PDBe Contact Form
online documentation	PDBe Documentation
online documentation	Depositing and Validating Data
online documentation	News
training	PDBe Training
twitter	@PDBeurope

Additional Information

Contact	PDBe Helpdesk
Identifiers.org	MIR:00100037

TeSS training resources

PDBe: Searching for biological macromolecular structures

PDBe: Exploring a Protein Data Bank (PDB) entry

PDBe: An introduction to search and entry pages: webinar

PDBe: Searching the Protein Data Bank

PDBe: Quick tour

Tools

EMDB	http://www.ebi.ac.uk/pdbe/emdb
PDBePISA	http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
wwPDB Validation Service	http://validate.wwpdb.org
Full PDBe Tools List	https://www.ebi.ac.uk/pdbe/services

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Curation

OneDep: Data Deposition Portal

http://deposit-pdbe.wwpdb.org/

Data Access

Download	ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb/data/structures/all
search by sequence	http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/
PDBeFold- Search by structure	http://www.ebi.ac.uk/msd-srv/ssm/
Search	http://www.pdbe.org

REST Web Services

REST calls based on PDB entry data

http://www.ebi.ac.uk/pdbe/api/doc/

Publications

PDBe: Protein Data Bank in Europe.

Velankar S., Alhroub Y., Best C., Caboche S., Conroy MJ., Dana JM., Fernandez Montecelo MA., van Ginkel G., Golovin A., Gore SP., Gutmanas A., Haslam P., Hendrickx PM., Heuson E., Hirshberg M., John M., Lagerstedt I., Mir S., Newman LE., Oldfield TJ., Patwardhan A., Rinaldi L., Sahni G., Sanz-García E., Sen S., Slowley R., Suarez-Uruena A., Swaminathan GJ., Symmons MF., Vranken WF., Wainwright M., Kleywegt GJ.,
Nucleic Acids Res. 2012

View Paper (PubMed) View Publication

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ.
Nucleic Acids Res. 2016

View Paper (PubMed) View Publication

The archiving and dissemination of biological structure data

Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar
Current Opinion in Structural Biology 2016

View Paper (PubMed) View Publication

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Mir S,Alhroub Y,Anyango S,Armstrong DR,Berrisford JM,Clark AR,Conroy MJ,Dana JM,Deshpande M,Gupta D,Gutmanas A,Haslam P,Mak L,Mukhopadhyay A,Nadzirin N,Paysan-Lafosse T,Sehnal D,Sen S,Smart OS,Varadi M,Kleywegt GJ,Velankar S
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

This record is maintained by PDBe

Funds

European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (Government body)
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
National Science Foundation (NSF), USA (Government body)
European Union (EU) (Government body)
Medical Research Council (MRC), London, UK (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA (Government body)
The Wellcome Trust, UK (Charitable foundation)

Maintains

European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute) Lead

Grant Number(s)

088944 (The Wellcome Trust, UK)
104948 (The Wellcome Trust, UK)
1RO1 GM079429-01A1 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)
226073 (European Union (EU))
284209 (European Union (EU))
675858 (European Union (EU))
BB/E007511/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/G022577/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/J007471/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/K016970/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/K020013/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/M011674/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/M011674/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/M013146/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/M020347/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/M020428/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
DBI-1338415 (National Science Foundation (NSF), USA)
GM079429 (National Institutes of Health (NIH), Bethesda, MD, USA)
MR/L007835/1 (Medical Research Council (MRC), London, UK)
R01GM079429-01A1 (National Institutes of Health (NIH), Bethesda, MD, USA)

Protein Data Bank in Europe

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