cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Nature Methods, Journal Year: 2017, Volume and Issue: 14(3), P. 290 - 296

Published: Feb. 6, 2017

Language: Английский

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New tools for automated high-resolution cryo-EM structure determination in RELION-3

eLife, Journal Year: 2018, Volume and Issue: 7

Published: Nov. 9, 2018

Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility use resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering execution jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation 3D-classification. Per-particle refinement CTF parameters correction estimated beam tilt higher resolution reconstructions when particles are at different heights ice, and/or coma-free alignment not optimal. Ewald sphere curvature improves for large particles. We illustrate these developments publicly available data sets: together a Bayesian approach beam-induced motion it leads improvements 0.2–0.7 Å compared previous RELION versions.

Language: Английский

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Structures and distributions of SARS-CoV-2 spike proteins on intact virions

Nature, Journal Year: 2020, Volume and Issue: 588(7838), P. 498 - 502

Published: Aug. 17, 2020

Language: Английский

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

eLife, Journal Year: 2016, Volume and Issue: 5

Published: Nov. 15, 2016

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 bottleneck that currently limiting throughput and development new methods. Here, we present an implementation RELION image processing software uses graphics processors (GPUs) to address most computationally intensive steps its workflow. Both classification high-resolution refinement have been accelerated more than order-of-magnitude, template-based particle selection well over two orders-of-magnitude on desktop hardware. Memory requirements GPUs reduced fit widely available hardware, show use single precision arithmetic does not adversely affect results. This enables in matter days workstation.

Language: Английский

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Structural basis of STING binding with and phosphorylation by TBK1

Nature, Journal Year: 2019, Volume and Issue: 567(7748), P. 394 - 398

Published: March 6, 2019

Language: Английский

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Processing of Structurally Heterogeneous Cryo-EM Data in RELION

Methods in enzymology on CD-ROM/Methods in enzymology, Journal Year: 2016, Volume and Issue: unknown, P. 125 - 157

Published: Jan. 1, 2016

Language: Английский

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Cryo-EM structures of STING reveal its mechanism of activation by cyclic GMP–AMP

Nature, Journal Year: 2019, Volume and Issue: 567(7748), P. 389 - 393

Published: March 6, 2019

Language: Английский

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Helical reconstruction in RELION

Journal of Structural Biology, Journal Year: 2017, Volume and Issue: 198(3), P. 163 - 176

Published: Feb. 11, 2017

We describe a new implementation for the reconstruction of helical assemblies in empirical Bayesian framework RELION. Our approach calculates optimal linear filters 3D by embedding symmetry operators Fourier-space, and deals with deviations from perfect through Gaussian-shaped priors on orientations individual segments. By incorporating our into standard pipeline single-particle analysis RELION, aims to be easily accessible non-experienced users. Although does not solve problem that grossly incorrect structures can obtained when wrong is imposed, we show four different test cases it capable reconstructing near-atomic resolution.

Language: Английский

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Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

eLife, Journal Year: 2018, Volume and Issue: 7

Published: June 1, 2018

Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe new tool, called multi-body refinement, which models flexible as user-defined number rigid bodies move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the tool generates reconstructions defined fully automated manner. Moreover, using principal component analysis on relative orientations over all particle images data set, we generate movies most important motions data. Our results two test cases, cytoplasmic ribosome Plasmodium falciparum, and spliceosomal B-complex yeast, illustrate how refinement can be useful to gain unique insights into structure dynamics large macromolecular complexes.

Language: Английский

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Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

Cell, Journal Year: 2016, Volume and Issue: 165(7), P. 1698 - 1707

Published: May 28, 2016

Language: Английский

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