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    Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy

    Joseph, Agnell Praveen and Lagerstedt, I. and Patwardhan, A. and Topf, Maya and Winn, M. (2017) Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. Journal of Structural Biology 199 (1), pp. 12-26. ISSN 1047-8477.

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    Abstract

    Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led to a rapid increase in the amount of volume data available for biomolecules. This creates a demand for better methods to analyse the data, including improved scores for comparison, classification and integration of data at different resolutions. To this end, we developed and evaluated a set of scoring functions that compare 3D-EM volumes. To test our scores we used a benchmark set of volume alignments derived from the Electron Microscopy Data Bank. We find that the performance of different scores vary with the map-type, resolution and the extent of overlap between volumes. Importantly, adding the overlap information to the local scoring functions can significantly improve their precision and accuracy in a range of resolutions. A combined score involving the local mutual information and overlap (LMI_OV) performs best overall, irrespective of the map category, resolution or the extent of overlap, and we recommend this score for general use. The local mutual information score itself is found to be more discriminatory than cross-correlation coefficient for intermediate-to-low resolution maps or when the map size and density distribution differ significantly. For comparing map surfaces, we implemented two filters to detect the surface points, including one based on the ‘extent of surface exposure’. We show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features. All the scores discussed are implemented in TEMPy (http://tempy.ismb.lon.ac.uk/).

    Metadata

    Item Type: Article
    Keyword(s) / Subject(s): 3D electron cryo-microscopy, Integrative modelling, Scoring functions, Macromolecular assemblies, Density fitting
    School: Birkbeck Schools and Departments > School of Science > Biological Sciences
    Depositing User: Administrator
    Date Deposited: 17 Jul 2017 12:35
    Last Modified: 14 May 2018 10:06
    URI: http://eprints.bbk.ac.uk/id/eprint/19170

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