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

Dari Kimanius; Bjorn O Forsberg; Sjors Scheres; Erik Lindahl

doi:10.1101/059717

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bioRxiv · 10.1101/059717

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

Dari Kimanius·Bjorn O Forsberg·Sjors Scheres·Erik Lindahl

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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 O_SCPCAPRELIONC_SCPCAP 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 up to 40-fold, and template-based particle selection has been accelerated almost 1000-fold on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hard-ware, 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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Dari Kimanius, Bjorn O Forsberg, Sjors Scheres, Erik Lindahl. 2016-06-19. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. https://doi.org/10.1101/059717

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