Advanced Electron Microscopy Techniques and Applications

Supervised Deep Learning for Efficient Cryo-EM Image Alignment in Drug Discovery with cryoPARES

The paper introduces cryoPARES, a deep learning method for efficient cryo-EM image alignment, enabling faster and automated structure determination with reduced manual intervention.

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-EM density maps

This study benchmarks deep learning methods for building atomic models from cryo-EM density maps, showing their superiority over traditional methods and the benefits of integrating AlphaFold.

Thickness and quality controlled fabrication of fluorescence-targeted frozen-hydrated lamellae

The paper presents three strategies for live feedback control during the fabrication of frozen-hydrated lamellae using cryogenic FIB-SEM, ensuring thickness and quality.

A correlative workflow streamlines synaptic imaging by cryo-electron tomography

The paper develops a correlative cryo-light/electron microscopy workflow to target and image synapses with cryo-ET, revealing excitatory synapses.

CryoSamba: self-supervised deep volumetric denoising for cryo-electron tomography data

CryoSamba improves cryo-ET image quality by denoising 3D volumes through self-supervised deep learning without requiring labels or synthetic data.

Cryo-EM Heterogeneity Analysis using Regularized Covariance Estimation and Kernel Regression

The paper introduces RECOVAR, a method for analyzing cryo-EM data heterogeneity using regularized covariance estimation and kernel regression, achieving high-resolution conformational state reconstruction and interpretable results.

CryoTEN: Efficiently Enhancing Cryo-EM DensityMaps Using Transformers

CryoTEN improves cryo-EM density maps using a transformer-based model, achieving better quality and faster performance than existing methods.

Deconvolution improves cryo-EM maps

This paper introduces a deconvolution method called AR-Decon to improve the quality of cryo-EM maps and shows it is robust and broadly applicable.

The graphene-based affinity cryo-EM grid for the endogenous protein structure determination

This paper introduces a graphene-based affinity cryo-EM grid (GFD-A) for capturing endogenous protein complexes, achieving resolutions of 2.71 Å for tagged proteins and 3.0–3.9 Å for endogenous RNase MRP and RNase P.

Combining MicroED and native mass spectrometry for structural discovery of enzyme-biosynthetic inhibitor complexes

This paper combines MicroED and native mass spectrometry to determine structures of enzyme-inhibitor complexes and identify high-affinity ligands from crude samples.

Complementary Volume Electron Microscopy-based approaches reveal ultrastructural changes in germline intercellular bridges of D. melanogaster

The paper uses volume electron microscopy techniques to study ultrastructural changes in germline intercellular bridges during Drosophila oogenesis, revealing new structural features and developmental patterns.

Ice Finder: Few-Shot Learning for Non-Vitrified Ice Segmentation

Ice Finder uses few-shot learning to segment non-vitrified ice in tomography, improving domain generalization and processing speed.

Making plant tissue accessible for cryo-electron tomography

This paper describes optimized cryo-ET sample preparation workflows for plant tissues, achieving subnanometer resolution through targeted FIB milling and lamella trimming.

SLICK: A Sandwich-LIke Culturing Kit for in situ Cryo-ET Sample Preparation

SLICK simplifies and increases throughput for in situ cryo-ET sample preparation.

MicroED Structures of Fluticasone Furoate and Fluticasone Propionate Provide New Insights to Their Function

This study uses MicroED and DFT to determine the 3D structures of fluticasone furoate and propionate in different states, revealing conformational changes and their functional implications.

Cryo-EM ligand building using generative AI and molecular dynamics

This paper develops a method combining generative AI and molecular dynamics to improve ligand modeling in cryo-EM maps of protein-ligand complexes.

Structural basis of flagellar rod assembly on the FliPQR protein-export channel

The paper presents a cryoEM structure of the FliPQR complex in closed form, revealing how FliE opens the periplasmic gate for flagellar rod assembly.

Modeling cryo-EM structures in alternative states with generative AI and density-guided simulations

The paper improves modeling of cryo-EM maps for membrane proteins with multiple states using generative AI and density-guided simulations.

CryoVIA - An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs

CryoVIA quantifies membrane structures from cryo-EM images by automating segmentation, structure identification, and analysis of membrane properties.

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes from Azotobacter vinelandii

The paper uses cryoEM and machine learning to identify and classify novel oligomeric protein complexes from Azotobacter vinelandii, revealing new structural states of proteins like phosphoglucoisomerase and pyridine transhydrogenase.

In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states

The paper presents an in silico method to classify and identify co-purified protein complexes using cryoEM data, revealing new structures and multiple membrane scaffold protein assembly states.

Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos

The paper introduces mito-SegEM, a method for efficiently mapping mitochondria in electron microscopy volumes using webKnossos, achieving accurate and efficient reconstruction across tissues.

Training Generalized Segmentation Networks with Real and Synthetic Cryo-ET data.

The paper trains segmentation networks for cryo-ET data using synthetic and real data, showing that synthetic data with molecular diversity improves performance but real data is needed for generalization.

Application of cryo-FIB-SEM for investigating organelle ultrastructure in guard cells of higher plants

This study uses cryo-FIB-SEM to visualize the ultrastructure of guard cells in Vicia faba, revealing subcellular organelles in a near-native state.

Rapid structural analysis of bacterial ribosomes in situ

The paper develops a rapid in situ cryo-ET workflow for bacterial ribosome structure analysis, achieving sub-nm resolution in E. coli within 10 days.

Protein identification using cryo-EM and artificial intelligence guides improved sample purification

This paper identifies an unknown contaminant in protein samples using Cryo-EM and AI tools, leading to improved purification protocols.

Cryo-electron tomography pipeline for plasma membranes.

This paper introduces a cryo-electron tomography pipeline for imaging plasma membranes with angstrom-scale resolution and targeted protein labeling.

VitisC: Visualizing interested target via integrated scaffold of cytoophidium

The paper introduces VitisC, a method to visualize small proteins using cryo-EM by attaching them to a filamentous scaffold formed by E. coli CTP synthase, achieving a resolution of 3.39 Å.

Observation of the protein-inorganic interface of ferritin by cryo-electron microscopy

This study uses cryo-EM to visualize the protein-inorganic interface of human light chain ferritin bound to iron oxide nanoparticles, revealing new interactions at the C-terminus.

Structural insights into the assembly mechanism of the flagellar MS-ring with three different symmetries

This paper reports cryoEM structures of the flagellar MS-ring and identifies how FliF subunits adopt different conformations to generate three rotational symmetries.