A self-supervised workflow for particle picking in cryo-EM

IUCrJ
Donal M McSweeneyQun Liu

Abstract

High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as Relion, cryoSPARC, cisTEM, SPHIRE and EMAN2.

References

Apr 7, 2004·Journal of Structural Biology·Yuanxin ZhuClinton S Potter
Apr 7, 2004·Journal of Structural Biology·Zhong Huang, Pawel A Penczek
Jul 25, 2006·Journal of Structural Biology·Guang TangSteven J Ludtke
Jul 28, 2006·Journal of Structural Biology·James Z Chen, Nikolaus Grigorieff
Nov 12, 2013·Nature Methods·Alp KucukelbirHemant D Tagare
Mar 13, 2014·Journal of Structural Biology·Robert LangloisJoachim Frank
Dec 9, 2014·Journal of Structural Biology·Sjors H W Scheres
Mar 23, 2015·Archives of Biochemistry and Biophysics·Richard Henderson
Apr 29, 2015·Journal of Structural Biology·Roberto MarabiniJose M Carazo
Nov 26, 2015·Journal of Structural Biology·Kai Zhang
Feb 13, 2016·IUCrJ·Sriram SubramaniamRichard Henderson
Jul 18, 2016·Journal of Structural Biology·Feng WangJianyang Zeng
Feb 7, 2017·Nature Methods·Ali PunjaniMarcus A Brubaker
Jun 6, 2017·Acta Crystallographica. Section D, Structural Biology·Rafael Fernandez-Leiro, Sjors H W Scheres
Mar 8, 2018·ELife·Timothy GrantNikolaus Grigorieff
May 13, 2019·Trends in Biochemical Sciences·Radostin DanevMasahide Kikkawa
Jun 27, 2019·Communications Biology·Thorsten WagnerStefan Raunser
Oct 9, 2019·Nature Methods·Dimitry Tegunov, Patrick Cramer
Dec 28, 2019·Proceedings of the National Academy of Sciences of the United States of America·Yimo HanNieng Yan
Jan 12, 2020·Communications Biology·Thorsten WagnerStefan Raunser

❮ Previous
Next ❯

Citations

Nov 13, 2020·Nature Communications·Markus StabrinStefan Raunser

❮ Previous
Next ❯

Methods Mentioned

BETA
feature extraction

Software Mentioned

Localpicker
TensorFlow
Kpicker
EMAN2
cisTEM
ResMap
Gctf
FastParticlePicker
SPHIRE
Relion

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
Donal M McSweeneyQun Liu
Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi
Xiaorong Wu, Xiaoming Wu
© 2021 Meta ULC. All rights reserved