M-free: Mask-independent scoring of the reference bias

Journal of Structural Biology
Michael KunzAchilleas S Frangakis

Abstract

The M-free score is a heuristic to measure the reference bias in applications such as template matching and sub-tomogram averaging. In the original formulation the mask typically used in these applications had to be separated into a working and a testing area. Here we present a variant of the calculation of the M-free score, which under certain conditions does not require adapting the mask used during the processing. This is made possible by a modified algorithm that allows for arbitrary variances in the testing and in the working area. Consequently, the reference bias can be estimated with knowledge of only the starting reference, the final average and the mask used for processing. We show that the new formulation of the M-free score gives a reliable measure of the reference bias for any sub-tomogram average that has ancillary data, such as when the averaged structure contains density in the periphery, when a complex is attached to a membrane (membrane-associated complexes) or when one subunit is attached to others (e.g. in viruses). Further, we show that in contrast to correlation-based measurements, the M-free score is sensitive to wrong-alignments and contaminations present in the data set. The scope of this new calculation...Continue Reading

References

Aug 1, 1982·Journal of Microscopy·W O Saxton, W Baumeister
Apr 26, 2003·Journal of Structural Biology·Tanvir R ShaikhJoachim Frank
Aug 29, 2006·PLoS Pathogens·Giulia ZanettiStephen D Fuller
Jun 26, 2007·Journal of Molecular Biology·Carsten SachseNikolaus Grigorieff
Aug 28, 2007·Journal of Structural Biology·Friedrich FörsterAchilleas S Frangakis
Aug 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Karen M DaviesWerner Kühlbrandt
May 27, 2014·Journal of Structural Biology·Zhou Yu, Achilleas S Frangakis
Jan 24, 2015·Science·Shoh AsanoWolfgang Baumeister

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Citations

Jun 13, 2017·Journal of Clinical Epidemiology·Bram DuyxMaurice P Zeegers
Aug 7, 2017·Biophysical Reports·Jesús G Galaz-Montoya, Steven J Ludtke
Oct 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Mateusz SikoraAchilleas S Frangakis

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