Likelihood-based signal and noise analysis for docking of models into cryo-EM maps

Read, Randy J.; Millán, Claudia; McCoy, Airlie J.; Terwilliger, Thomas C.

doi:10.1107/s2059798323001596

Likelihood-based signal and noise analysis for docking of models into cryo-EM maps

Journal Article · Wed Mar 15 00:00:00 EDT 2023 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/s2059798323001596· OSTI ID:2470495

^[1]; ^[2]; McCoy, Airlie J. ^[1]; ^[3]

University of Cambridge (United Kingdom)
University of Cambridge (United Kingdom); Wellcome Genome Campus, Cambridge (United Kingdom)
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding applications in both crystallography and cryo-EM. Indeed, previous crystallographic work on the errors in structural models is directly applicable to likelihood targets in cryo-EM. Likelihood targets in Fourier space are derived here to characterize, based on the comparison of half-maps, the direction- and resolution-dependent variation in the strength of both signal and noise in the data. Because the signal depends on local features, the signal and noise are analysed in local regions of the cryo-EM reconstruction. The likelihood analysis extends to prediction of the signal that will be achieved in any docking calculation for a model of specified quality and completeness. A related calculation generalizes a previous measure of the information gained by making the cryo-EM reconstruction.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: National Institutes of Health, National Institute of General Medical Sciences; USDOE; Wellcome Trust

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 2470495

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Issue: 4 Vol. 79; ISSN 2059-7983

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biophysics
Cryo-EM
Crystallography
Docking
Information gain
Likelihood

Likelihood-based signal and noise analysis for docking of models into cryo-EM maps

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