Journal Article

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

Kimanius, Dari, Forsberg, Björn O, Scheres, Sjors HW, Lindahl, Erik

2016

Overview

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.

• Publisher: eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Algorithms / Biochemistry towards Bioinformatics / biokemi med inriktning mot bioinformatik / Biophysics and Structural Biology / Classification / Computational Biology - methods / Computer applications / cryo-EM / Cryoelectron Microscopy - methods / Datasets / Fourier transforms / GPU / Image processing / Image Processing, Computer-Assisted - methods / image reconstruction / Laboratories / Mathematics / micrograph / refinement / Software / Solvents / Standard deviation / Time Factors / Tools and Resources