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

Elife. 2016 Nov 15;5:e18722. doi: 10.7554/eLife.18722.

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.

Keywords: GPU; biophysics; classification; cryo-EM; image reconstruction; micrograph; none; refinement; structural biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Cryoelectron Microscopy / methods*
  • Image Processing, Computer-Assisted / methods*
  • Time Factors