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Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

Open access
Kimanius, Dari, Forsberg, Björn O, Scheres, Sjors HW, Lindahl, Erik·2016·eLife
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 large computational costs, which has introduced 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 well over 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.

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Cited by

Metadata

Authors
Kimanius, D., Forsberg, B. O., Scheres, S. H., & Lindahl, E.
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2016-11-15
Volume
5
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.18722
OpenAlex
W2432427150
Cited by
901
References
2
FWCI
80.74
Type
journal article
Language
en
Open access
gold
Licence
Funders
  • Medical Research Council (MC UP A025 1013)
  • Vetenskapsrådet (2013-5901)
  • Horizon 2020 (EINFRA-2015-1-675728)
  • Swedish e-Science Research Centre
  • Swedish National Infrastructure for Computing (2015/16-45)

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