Community recommendations on cryoEM data archiving and validation

Bibliographic Details
Title: Community recommendations on cryoEM data archiving and validation
Authors: Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Catherine L. Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H. W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar
Source: IUCrJ, Vol 11, Iss 2, Pp 140-151 (2024)
Publisher Information: International Union of Crystallography, 2024.
Publication Year: 2024
Collection: LCC:Crystallography
Subject Terms: cryogenic-specimen electron microscopy, data archiving, validation, quality control, electron microscopy data bank, protein data bank, single-particle cryoem, databases, bioinformatics, structure determination, Crystallography, QD901-999
More Details: In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 2052-2525
20522525
Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252524001246; https://doaj.org/toc/2052-2525
DOI: 10.1107/S2052252524001246
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  Data: IUCrJ, Vol 11, Iss 2, Pp 140-151 (2024)
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  Data: In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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  Data: 2052-2525<br />20522525
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  Data: http://scripts.iucr.org/cgi-bin/paper?S2052252524001246; https://doaj.org/toc/2052-2525
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