Likelihood-based docking of models into cryo-EM maps

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

doi:10.1107/s2059798323001602

Likelihood-based 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/s2059798323001602· OSTI ID:2470496

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

University of Cambridge (United Kingdom); SciBite Limited, Cambridge (United Kingdom)
University of Cambridge (United Kingdom)
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

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.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: National Institutes of Health (NIH); USDOE; Wellcome Trust

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 2470496

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 docking of models into cryo-EM maps

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