16076

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

Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Sweden
bioRxiv preprint, (19 Jun 2016)
@article{kimanius2016accelerated,

   title={Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2},

   author={Kimanius, Dari and Forsberg, Bjorn O and Scheres, Sjors and Lindahl, Erik},

   journal={bioRxiv},

   pages={059717},

   year={2016},

   publisher={Cold Spring Harbor Labs Journals}

}

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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 work-flow. 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 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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