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

Kimanius D, Forsberg BO, Scheres SH, Lindahl E

Elife 5 (-) - [2016-11-15; online 2016-11-15]

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.

Affiliated researcher

PubMed 27845625

DOI 10.7554/eLife.18722

Crossref 10.7554/eLife.18722

pmc: PMC5310839

Publications 9.5.0