The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Measurement of atom resolvability in cryo-EM maps with Q-scores
Open accessAbstract
Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q -score. Q -scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q -scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q -scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q -scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q -score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms. Q -scores provide a quantitative metric for resolvability in cryo-EM maps, and can be used at the atom, residue or macromolecule scale.
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Cites
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PHENIX : a comprehensive Python-based system for macromolecular structure solution
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MolProbity : all-atom structure validation for macromolecular crystallography
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Cited by
Automated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686
Automated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2024) · Nature · doi:10.1038/s41586-024-07215-4 · Cited by 686
Assessment of three‐dimensional RNA structure prediction in CASP15
Das, R., Kretsch, R. C., Simpkin, A. J., Mulvaney, T., Pham, P., Rangan, R., Bu, F., Keegan, R. M., Topf, M., Rigden, D. J., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26602 · Cited by 139
Structural basis for strand-transfer inhibitor binding to HIV intasomes
Passos, D. O., Li, M., Jóźwik, I. K., Zhao, X. Z., Santos-Martins, D., Yang, R., Smith, S. J., Jeon, Y., Forli, S., Hughes, S. H., et al. (2020) · Science · doi:10.1126/science.aay8015 · Cited by 106
Progressive assembly of multi-domain protein structures from cryo-EM density maps
Zhou, X., Li, Y., Zhang, C., Zheng, W., Zhang, G., & Zhang, Y. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00232-1 · Cited by 75
Metadata
- Authors
- Pintilie, G., Zhang, K., Su, Z., Li, S., Schmid, M. F., & Chiu, W.
- Venue
- Nature Methods
- Published
- 2020-02-10
- Volume
- 17
- Issue
- 3
- Pages
- 328-334
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W3005016287
- Cited by
- 400
- References
- 3
- FWCI
- 17.49
- Type
- journal article
- Language
- en
- Open access
- green
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