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Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
Number of Authors: 4
2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, e18722Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 5, e18722
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-141500DOI: 10.7554/eLife.18722ISI: 000394244600001OAI: oai:DiVA.org:su-141500DiVA: diva2:1087112
Available from: 2017-04-05 Created: 2017-04-05 Last updated: 2017-04-05Bibliographically approved

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Kimanius, DariForsberg, Björn O.Lindahl, Erik
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