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Model Archive

General Information

The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts.

Homepage https://www.modelarchive.org/

Countries that developed this resource Switzerland , United States

Created in 2013

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: Model Archive; Model Archive; DOI: https://doi.org/10.25504/FAIRsharing.tpqndj; Last edited: June 22, 2020, 11:59 a.m.; Last accessed: Aug 06 2020 10:42 a.m.

This record is maintained by Torsten ORCID and gerardo.tauriello@unibas.ch

Record added: Dec. 9, 2015, 3:29 p.m.
Record updated: June 22, 2020, 11:59 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.tpqndj' by 'The FAIRsharing Team' at 11:59, 22 Jun 2020 (approved):

	'related_databases' has been modified:
		Before:
			Protein Model Database
			Molecular Modeling Database (MMDB)
			SWISS-MODEL Repository of 3D protein structure models
			ModBase database of comparative protein structure models
		After:
			Molecular Modeling Database (MMDB)
			SWISS-MODEL Repository of 3D protein structure models
			ModBase database of comparative protein structure models
		Added:
		Removed:
			Protein Model Database

Edits to 'https://fairsharing.org/FAIRsharing.tpqndj' by 'The FAIRsharing Team' at 11:56, 22 Jun 2020 (approved):

	'description' has been modified:
		Before: The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts. Model Archive is part of the Protein Model Portal (http://www.proteinmodelportal.org). 
		After: The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts.

Edits to 'https://fairsharing.org/FAIRsharing.tpqndj' by 'The FAIRsharing Team' at 11:56, 22 Jun 2020 (approved):

	'organizations' has been modified:
		Before:
			Biozentrum, University of Basel, Basel, Switzerland|http://www.biozentrum.unibas.ch/research/groups-platforms/overview/unit/schwede/|Maintains
			Swiss Institute of Bioinformatics (SIB)|http://www.sib.swiss/|Maintains
			National Institutes of Health (NIH), Bethesda, MD, USA|https://www.nih.gov/|Funds
		After:
			National Institutes of Health (NIH), Bethesda, MD, USA|https://www.nih.gov/|Funds
			Biozentrum, University of Basel, Basel, Switzerland|http://www.biozentrum.unibas.ch/research/groups-platforms/overview/unit/schwede/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains,Funds
		Added:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains,Funds
		Removed:
			Swiss Institute of Bioinformatics (SIB)|http://www.sib.swiss/|Maintains

	'standardsImplemented' has been modified:
		Before:
			Protein Data Bank Format
		After:
			Protein Data Bank Format
			Digital Object Identifier
		Added:
			Digital Object Identifier
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			email|help-modelarchive@unibas.ch
			help|https://www.modelarchive.org/help
		Added:
			email|help-modelarchive@unibas.ch
			help|https://www.modelarchive.org/help
		Removed:

	'name' has been modified:
		Before: Model Archive - theoretical models of macromolecular structures 
		After: Model Archive

	'tools' has been modified:
		Before:
			Structural Biology Knowledgebase||http://sbkb.org/
			Protein Model Portal||http://www.proteinmodelportal.org/
		After:
		Added:
		Removed:
			Structural Biology Knowledgebase||http://sbkb.org/
			Protein Model Portal||http://www.proteinmodelportal.org/

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Structural Biology
		Added:
			Structural Biology
		Removed:
			Life Science

	'onto_domains' has been modified:
		Before:
			Mathematical model
			Prediction and recognition
			Protein structure
			modeling and simulation objective
			protein
			structure
		After:
			Mathematical model
			Prediction and recognition
			Protein structure
			Structure
			modeling and simulation objective
			protein
			structure
		Added:
			Structure
		Removed:

	'dataProcesses' has been modified:
		Before:
			Model Deposition, data curation, http://www.modelarchive.org/project/step1
			web interface, data access, http://www.modelarchive.org/
		After:
			Model Deposition, data curation, https://www.modelarchive.org/projects/new/basic
			Search, data access, https://www.modelarchive.org/
		Added:
			Model Deposition, data curation, https://www.modelarchive.org/projects/new/basic
			Search, data access, https://www.modelarchive.org/
		Removed:
			Model Deposition, data curation, http://www.modelarchive.org/project/step1
			web interface, data access, http://www.modelarchive.org/

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

	'publications' has been modified:
		Before:
			Outcome of a workshop on applications of protein models in biomedical research.|Schwede T,Sali A,Honig B,Levitt M,Berman HM,Jones D,Brenner SE,Burley SK,Das R,Dokholyan NV,Dunbrack RL Jr,Fidelis K,Fiser A,Godzik A,Huang YJ,Humblet C,Jacobson MP,Joachimiak A,Krystek SR Jr,Kortemme T,Kryshtafovych A,Montelione GT,Moult J,Murray D,Sanchez R,Sosnick TR,Standley DM,Stouch T,Vajda S,Vasquez M,Westbrook JD,Wilson IA|Structure|2009
			The Protein Model Portal--a comprehensive resource for protein structure and model information.|Haas J,Roth S,Arnold K,Kiefer F,Schmidt T,Bordoli L,Schwede T|Database (Oxford)|2013
		After:
			The Protein Model Portal--a comprehensive resource for protein structure and model information.|Haas J,Roth S,Arnold K,Kiefer F,Schmidt T,Bordoli L,Schwede T|Database (Oxford)|2013
			Outcome of a workshop on applications of protein models in biomedical research.|Schwede T,Sali A,Honig B,Levitt M,Berman HM et al.|Structure|2009
		Added:
			Outcome of a workshop on applications of protein models in biomedical research.|Schwede T,Sali A,Honig B,Levitt M,Berman HM et al.|Structure|2009
		Removed:
			Outcome of a workshop on applications of protein models in biomedical research.|Schwede T,Sali A,Honig B,Levitt M,Berman HM,Jones D,Brenner SE,Burley SK,Das R,Dokholyan NV,Dunbrack RL Jr,Fidelis K,Fiser A,Godzik A,Huang YJ,Humblet C,Jacobson MP,Joachimiak A,Krystek SR Jr,Kortemme T,Kryshtafovych A,Montelione GT,Moult J,Murray D,Sanchez R,Sosnick TR,Standley DM,Stouch T,Vajda S,Vasquez M,Westbrook JD,Wilson IA|Structure|2009

	'homepage' has been modified:
		Before: http://www.modelarchive.org/
		After: https://www.modelarchive.org/

Edits to 'https://fairsharing.org/FAIRsharing.tpqndj' by 'The FAIRsharing Team' at 11:28, 30 Aug 2016 (approved):

	'description' has been modified:
		Before: The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. Besides the actual model coordinates, archived models should include sufficient details about assumptions, parameters and constraints applied in the simulation to allow the user of a model to assess and if necessary reproduce the simulation. Since 2006, only structures that have been determined experimentally are allowed to be deposited in the PDB, and theoretical models of macromolecular structures are no longer part of the PDB archive. The Model Archive is being developed following a community recommendation during a workshop on applications of protein models in biomedical research as part of Protein Model Portal.
		After: The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts. Model Archive is part of the Protein Model Portal (http://www.proteinmodelportal.org).  Domain list has changed:  Previous values: 3D structural data including 3D coordinates|| Computational model|property|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2300 Computational predictions|| Protein|material|http://purl.org/obo/owl/GO#GO_0003675 Protein 3D structure|| Simulation|property| Structural model|| Structure data|information content entity|http://purl.org/obo/owl/PATO#PATO_0000141 New values:  3D structural data including 3D coordinates|| Computational model|property|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2300 Computational predictions|| Protein|material|http://purl.org/obo/owl/GO#GO_0003675 Protein 3D structure|| Simulation|property| Structural model|| Structure data|information content entity|http://purl.org/obo/owl/PATO#PATO_0000141 Life Science|domain| Publication List has changed:  Previous values: New values:  Outcome of a workshop on applications of protein models in biomedical research. The Protein Model Portal--a comprehensive resource for protein structure and model information. Organisations have changed:  Previous values: US National Institutes of Health (NIH) New values:  US National Institutes of Health (NIH) SIB|Swiss Institute of Bioinformatics Biozentrum|University of Basel

In Collections

Bioschemas

RDA Covid-19 WG Resources

Support

General

support email	General Contact
help	Help Diagram

Additional Information

Contact

Torsten Schwede ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Data Curation

Model Deposition

https://www.modelarchive.org/projects/new/basic

Data Access

https://www.modelarchive.org/

Publications

The Protein Model Portal--a comprehensive resource for protein structure and model information.

Haas J,Roth S,Arnold K,Kiefer F,Schmidt T,Bordoli L,Schwede T
Database (Oxford) 2013

View Paper (PubMed) View Publication

Outcome of a workshop on applications of protein models in biomedical research.

Schwede T,Sali A,Honig B,Levitt M,Berman HM et al.
Structure 2009

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Protein Data Bank Format

Identifier Schemas

Digital Object Identifier

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by Torsten ORCID and gerardo.tauriello@unibas.ch

Funds

National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute)

Maintains

Biozentrum, University of Basel, Basel, Switzerland (Lab) Lead
Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute)

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