New tools for automated cryo-EM single-particle analysis in RELION-4.0

2021/11/16 by Dari Kimanius, Liyi Dong, Grigory Sharov +2 · 11 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · #Advanced Electron Microscopy Techniques and Applications #Electron and X-Ray Spectroscopy Techniques #RNA modifications and cancer

paper · pdf · doi:10.1042/bcj20210708

openalex publication_date 2021/11/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/02

Abstract

We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient descent algorithm with adaptive moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on 12 publicly available cryo-EM data sets.

Citations

• UCSF Chimera—A visualization system for exploratory research and analysis

Cited by

• Calicivirus assembly and stability are mediated by the N-terminal domain of the capsid protein with the involvement of the viral genome
• Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models
• A dual-factor complex governs archaeal ribosome hibernation by sensing energy status
• CryoSift : an accessible and automated CNN-driven tool for cryo-EM 2D class selection
• Structural switch in acetylcholine receptors in developing muscle
• A natural depsipeptide antibiotic binds the E-site of the bacterial ribosome
• Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase
• Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P. furiosus
• The Impact of Digitalized Data Management on Materials Systems Workflows
• Use of hydrogen deuterium exchange mass spectrometry in tandem with modern structural biology
• A molecular stabiliser of an inhibitory eIF2B-eIF2(αP) complex activates the Integrated Stress Response

Related

• CryoSift : an accessible and automated CNN-driven tool for cryo-EM 2D class selection
• Learning to automate cryo-electron microscopy data collection with Ptolemy
• DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM
• CryoRL: Reinforcement Learning Enables Efficient Cryo-EM Data Collection
• CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders