Evidence map›Paper›PMID 38076521›Full record

ArticleArXiv2024

Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

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 and 37 more

Abstract readPreprint
PubMed Full text at PMC
In one paragraph

Article in ArXiv, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

47 authors.

Gerard J KleywegtEMBL-EBI, Cambridge, UK.
Paul D AdamsLawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA.
Sarah J ButcherUniversity of Helsinki, Helsinki, Finland.
Catherine L LawsonRCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA.
Alexis RohouGenentech, South San Francisco, California, USA.
Peter B RosenthalThe Francis Crick Institute, London, UK.
Sriram SubramaniamUniversity of British Columbia, Vancouver, BC, Canada.
Maya TopfBirkbeck, University of London, London, UK.
Sanja AbbottEMBL-EBI, Cambridge, UK.
Philip R BaldwinThe Salk Institute for Biological Studies, La Jolla, CA, USA.
John M BerrisfordEMBL-EBI, Cambridge, UK.
Gérard BricogneGlobal Phasing Limited, Cambridge, UK.
Preeti ChoudharyEMBL-EBI, Cambridge, UK.
Tristan I CrollUniversity of Cambridge, Cambridge, UK.
Radostin DanevThe University of Tokyo, Tokyo, Japan.
Sai J GanesanUniversity of California at San Francisco, San Francisco, CA, USA.
Timothy GrantMorgridge Institute for Research, Madison, WI, USA.
Aleksandras GutmanasEMBL-EBI, Cambridge, UK.
Richard HendersonMRC Laboratory of Molecular Biology, Cambridge, UK.
J Bernard HeymannNational Institutes of Health, Bethesda, MD, USA.
Juha T HuiskonenUniversity of Helsinki, Helsinki, Finland.
Andrei IstrateEMBL-EBI, Cambridge, UK.
Takayuki KatoOsaka University, Suita, Osaka, Japan.
Gabriel C LanderScripps Research, La Jolla, CA, USA.
Shee-Mei LokDuke-NUS Medical School, Singapore.
Steven J LudtkeBaylor College of Medicine, Houston, TX, USA.
Garib N MurshudovMRC Laboratory of Molecular Biology, Cambridge, UK.
Ryan PyeEMBL-EBI, Cambridge, UK.
Grigore D PintilieStanford University, Stanford, CA, USA.
Jane S RichardsonDuke University, Durham, NC, USA.
Carsten SachseForschungszentrum Jülich, Germany.
Osman SalihEMBL-EBI, Cambridge, UK.
Sjors H W ScheresMRC Laboratory of Molecular Biology, Cambridge, UK.
Gunnar F SchroederForschungszentrum Jülich, Germany.
Carlos Oscar S SorzanoNational Center of Biotechnology (CSIC), Madrid, Spain.
Scott M StaggFlorida State University, Tallahassee, FL, USA.
Zhe WangEMBL-EBI, Cambridge, UK.
Rangana WarshamanageMRC Laboratory of Molecular Biology, Cambridge, UK.
John D WestbrookRCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA.
Martyn D WinnScience and Technology Facilities Council, Research Complex at Harwell, Oxon, UK.
Jasmine Y YoungRCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA.
Stephen K BurleyRCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA.
Jeffrey C HochUConn Health, USA.
Genji KurisuOsaka University, Suita, Osaka, Japan.
Kyle MorrisEMBL-EBI, Cambridge, UK.
Ardan PatwardhanEMBL-EBI, Cambridge, UK.
Sameer VelankarEMBL-EBI, Cambridge, UK.

Funding

PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3M
Unified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6M
Biological Magnetic Resonance Data BankR24GM150793 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI JEFFREY C HOCH · 2023 to 2026
$3.0M
NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM133198NIGMS NIH HHS R24 GM150793Wellcome Trust
6 · The paper itself

Abstract

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for 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 consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

Indexed as

Cryogenic-specimen Electron Microscopydata archivingElectron Microscopy Data BankProtein Data Bankquality controlvalidation

Identifiers

PMID38076521
PMCPMC10705588

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.