1. Structural Biology and Molecular Biophysics
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Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

  1. Dari Kimanius
  2. Björn O Forsberg
  3. Sjors HW Scheres  Is a corresponding author
  4. Erik Lindahl  Is a corresponding author
  1. Stockholm University, Sweden
  2. MRC Laboratory of Molecular Biology,, United Kingdom
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Cite this article as: eLife 2016;5:e18722 doi: 10.7554/eLife.18722
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Abstract

By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at increased computational costs, introducing a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

Data availability

The following data sets were generated
The following previously published data sets were used
    1. Scheres SH
    (2014) Beta-galactosidase Falcon-II micrographs plus manually selected coordinates by Richard Henderson
    Publicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10017).
    https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10017/

Article and author information

Author details

  1. Dari Kimanius

    Department of Biochemistry and Biophysics, Science for Life Laboratory,, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.

  2. Björn O Forsberg

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.

  3. Sjors HW Scheres

    MRC Laboratory of Molecular Biology,, Cambridge, United Kingdom
    For correspondence
    scheres@mrc-lmb.cam.ac.uk
    Competing interests
    Sjors HW Scheres, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0462-6540

  4. Erik Lindahl

    Department of Biochemistry and Biophysics, Science for Life Laboratory,, Stockholm University, Stockholm, Sweden
    For correspondence
    erik.lindahl@dbb.su.se
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2734-2794

Funding

Medical Research Council (MC UP A025 1013)

  • Sjors HW Scheres

Vetenskapsrådet (2013-5901)

  • Erik Lindahl

Horizon 2020 (EINFRA-2015-1-675728)

  • Erik Lindahl

Swedish e-Science Research Centre

  • Erik Lindahl

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Sriram Subramaniam, National Cancer Institute, United States

Publication history

  1. Received: June 11, 2016
  2. Accepted: November 14, 2016
  3. Accepted Manuscript published: November 15, 2016 (version 1)
  4. Version of Record published: February 15, 2017 (version 2)

Copyright

© 2016, Kimanius et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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