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Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm University, Sweden.ORCID iD: 0000-0002-2734-2794
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
eLife Sciences Publications Ltd , 2016. Vol. 5, e18722
National Category
Medical Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-203846DOI: 10.7554/eLife.18722ISI: 000394244600001Scopus ID: 2-s2.0-85009208040OAI: oai:DiVA.org:kth-203846DiVA: diva2:1083168
Note

QC 20170320

Available from: 2017-03-20 Created: 2017-03-20 Last updated: 2017-11-29Bibliographically approved

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Lindahl, Erik

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