Likelihood-based docking of models into cryo-EM maps
Open accessPublished version of a preprint
Abstract
Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Assessing the utility of <scp>CASP14</scp> models for molecular replacement
Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26214 · Cited by 62 · see citing works
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- Authors
- Millán, C., McCoy, A. J., Terwilliger, T. C., & Read, R. J.
- Affiliations
- University of Cambridge (GB)
- Los Alamos National Laboratory (US)
- Corresponding author
- Read, Randy J.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2023-03-15
- Volume
- 79
- Issue
- 4
- Pages
- 281-289
- ISSN
- 2059-7983 (ISSN-L)
- PMC
- PMC10071562
- OpenAlex
- W4324304869
- Cited by
- 23
- References
- 2
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 8 · 2023: 4
- FWCI
- 2.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Acta Crystallographica Section D Structural Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Apollo
- Funders
- Wellcome Trust (209407/Z/17/Z)
- National Institutes of Health, National Institute of General Medical Sciences (P01GM063210)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- model orientation, rigid-body refinement, map resolution, model placement
- MeSH terms
- Models, Molecular, Protein Conformation, Proteins, Likelihood Functions, Crystallography, X-Ray, Cryoelectron Microscopy
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