Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F86652036%3A_____%2F24%3A00604480" target="_blank" >RIV/86652036:_____/24:00604480 - isvavai.cz</a>
Result on the web
<a href="https://www.nature.com/articles/s41592-024-02321-7" target="_blank" >https://www.nature.com/articles/s41592-024-02321-7</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41592-024-02321-7" target="_blank" >10.1038/s41592-024-02321-7</a>
Alternative languages
Result language
angličtina
Original language name
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
Original language description
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 & Aring) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10609 - Biochemical research methods
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Nature Methods
ISSN
1548-7091
e-ISSN
1548-7105
Volume of the periodical
21
Issue of the periodical within the volume
7
Country of publishing house
US - UNITED STATES
Number of pages
24
Pages from-to
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UT code for WoS article
001254026100002
EID of the result in the Scopus database
2-s2.0-85196858277