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MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudo-Symmetries

View ORCID ProfileAntoniya A. Aleksandrova, View ORCID ProfileEdoardo Sarti, View ORCID ProfileLucy R. Forrest
doi: https://doi.org/10.1101/653295
Antoniya A. Aleksandrova
Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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  • ORCID record for Antoniya A. Aleksandrova
Edoardo Sarti
Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Lucy R. Forrest
Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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  • For correspondence: lucy.forrest@nih.gov
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Abstract

In membrane proteins, symmetry and pseudo-symmetry often have functional or evolutionary implications. However, available symmetry detection methods have not been tested systematically on this class of proteins due to the lack of an appropriate benchmark set. Here we present MemSTATS, a publicly-available benchmark set of both quaternary and internal symmetries in membrane protein structures described in terms of order, repeated elements, and orientation of the axis with respect to the membrane plane. Moreover, using MemSTATS, we compare the performance of four widely-used symmetry detection algorithms and highlight specific challenges and areas for improvement in the future.

Footnotes

  • antoniya.aleksandrova{at}nih.gov, edoardo.sarti{at}nih.gov, lucy.forrest{at}nih.gov.

  • https://doi.org/10.5281/zenodo.3234036

  • https://github.com/AntoniyaAleksandrova/MemSTATS_benchmark

  • https://doi.org/10.5281/zenodo.3228540

  • Abbreviations

    MemSTATS
    Membrane protein Structures And Their Symmetries
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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    Posted May 29, 2019.
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    MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudo-Symmetries
    Antoniya A. Aleksandrova, Edoardo Sarti, Lucy R. Forrest
    bioRxiv 653295; doi: https://doi.org/10.1101/653295
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    MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudo-Symmetries
    Antoniya A. Aleksandrova, Edoardo Sarti, Lucy R. Forrest
    bioRxiv 653295; doi: https://doi.org/10.1101/653295

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