RT Journal Article
SR Electronic
T1 Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 059717
DO 10.1101/059717
A1 Dari Kimanius
A1 Björn O Forsberg
A1 Sjors HW Scheres
A1 Erik Lindahl
YR 2016
UL http://biorxiv.org/content/early/2016/06/19/059717.abstract
AB 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 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.