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

Author:

Kimanius Dari1,Forsberg Björn O1,Scheres Sjors HW2ORCID,Lindahl Erik13ORCID

Affiliation:

1. Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden

2. MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

3. Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden

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.

Funder

Medical Research Council

Vetenskapsrådet

Horizon 2020

Swedish e-Science Research Centre

Swedish National Infrastructure for Computing

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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