Acta Crystallographica Section D
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Acta Crystallographica Section D: Biological Crystallography welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure-function articles that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such articles should present new insights into biology, chemistry or structure. Articles on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Articles on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability.enCopyright (c) 2023 International Union of Crystallography2023-03-15International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:2059-7983Acta Crystallographica Section D: Biological Crystallography welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure-function articles that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such articles should present new insights into biology, chemistry or structure. Articles on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Articles on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability.text/htmlActa Crystallographica Section D: Structural Biology, Volume 79, Part 4, 2023textweekly12002-01-01T00:00+00:004792023-03-15Copyright (c) 2023 International Union of CrystallographyActa Crystallographica Section D: Structural Biology198urn:issn:2059-7983med@iucr.orgMarch 20232023-03-15Acta Crystallographica Section Dhttp://journals.iucr.org/logos/rss10d.gif
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Still imageLikelihood-based signal and noise analysis for docking of models into cryo-EM maps
http://scripts.iucr.org/cgi-bin/paper?vo5011
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.Copyright (c) 2023 International Union of Crystallographyurn:issn:2059-7983Read, R.J.Millán, C.McCoy, A.J.Terwilliger, T.C.2023-03-15doi:10.1107/S2059798323001596International Union of CrystallographyLikelihood-based rotation, translation and refinement targets have been derived for docking models into cryo-EM reconstructions.ENlikelihoodcryo-EMdockinginformation gainFast, 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.text/htmlLikelihood-based signal and noise analysis for docking of models into cryo-EM mapstext4792023-03-15Copyright (c) 2023 International Union of CrystallographyActa Crystallographica Section Dresearch papers00Likelihood-based docking of models into cryo-EM maps
http://scripts.iucr.org/cgi-bin/paper?vo5012
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.Copyright (c) 2023 International Union of Crystallographyurn:issn:2059-7983Millán, C.McCoy, A.J.Terwilliger, T.C.Read, R.J.2023-03-15doi:10.1107/S2059798323001602International Union of CrystallographyExploiting analogies to crystallographic molecular replacement, a strategy for docking into cryo-EM maps is informed by the calculation of expected log-likelihood-gain scores.ENlikelihoodcryo-EMdockinginformation gainOptimized 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.text/htmlLikelihood-based docking of models into cryo-EM mapstext4792023-03-15Copyright (c) 2023 International Union of CrystallographyActa Crystallographica Section Dresearch papers00