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Likelihood-based docking of models into cryo-EM maps
Open accessPreprint — published as 10.1107/s2059798323001602 · Paper page
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. Optimised 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. Synopsis: Exploiting analogies to crystallographic molecular replacement, a strategy for docking into cryo-EM maps is informed by calculations of expected log-likelihood-gain scores.
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Metadata
- 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
- Publisher
- openRxiv
- Published
- 2022-12-20
- Volume
- 79
- Issue
- 4
- Pages
- 281-289
- ISSN
- 2059-7983 (ISSN-L)
- PMC
- PMC10071562
- OpenAlex
- W4324304869
- Cited by
- 23
- References
- 1
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 8 · 2023: 4
- FWCI
- 2.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- 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 (Z/17/Z, 209407/Z/17/Z, 209407)
- National Institutes of Health (GM063210)
- National Institute of General Medical Sciences (P01GM063210, GM063210)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › 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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