Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
By Dari Kimanius, Björn Forsberg, Sjors H. W. Scheres, Erik Lindahl. 2016
972 citations recorded by the source corpus.
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.
Subfields: Materials Chemistry, Molecular Biology, Structural Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Tom Burnley
- Sjors H. W. Scheres
- S. W. Hoh
- Dari Kimanius
- Erik Lindahl
- Björn Forsberg
- Takanori Nakane
- W. Hagen
In Molecular Biology
- Tom Burnley
- S. W. Hoh
- M. A. Tortorici
- Takanori Nakane
- Sjors H. W. Scheres
- Dari Kimanius
- Joost Snijder
- Erik Lindahl
In Structural Biology
- Sjors H. W. Scheres
- Dari Kimanius
- Takanori Nakane
- Erik Lindahl
- Björn Forsberg
- W. Hagen
- Jasenko Zivanov
- M. A. Tortorici
Citations in the corpus
- New tools for automated high-resolution cryo-EM structure determination in RELION-3 (2018, methodology): “In RELION-2, a new code-path was introduced, which off-loaded the core computations onto graphical processing units (GPUs) ( Kimanius et al., 2016 ).”
- Helical reconstruction in RELION (2016, neutral): “The approach described in this paper has been implemented in RELION version 2.0, and was accelerated for execution on graphics cards along with the code for standard single-particle analysis of asymmetric particles (Kimanius et al., 2016).”
- Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors (2018, neutral): “ID=KRE6P5E8Z COOT Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/ pemsley/coot/ PHENIX Adams et al., 2010 http://www.phenix-online.org/ PyMOL Open-Source PyMOL 1.8.x http://www.pymol.org/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ Leginon Suloway et al., 2005 ”
- Advances in methods for atomic resolution macromolecular structure determination (2020, methodology): “Cryo-EM software developers have capitalized on high-performance GPU computing 14–16 , cloud computing 17,18 , and machine learning approaches for nearly user-free data processing 19–21 .”
- Glycan Shield and Fusion Activation of a Deltacoronavirus Spike Glycoprotein Fine-Tuned for Enteric Infections (2017, background): “0(68) with a box size of 640 490 pixels(2) and a pixel size of 0.”