Advanced Electron Microscopy Techniques and Applications

Light 'em up: efficient screening of gold grids in cryo-EM

The paper introduces an energy filter-based plasmon imaging method to efficiently screen gold grids in cryo-EM for optimal ice thickness.

Validation analysis of EMDB entries

The paper describes a three-tiered validation system for cryo-EM structures in EMDB, focusing on data quality and model fitting, with tier 1 providing extensive metrics and tier 3 integrating with wwPDB.

Analytic representation of inhomogeneous-resolution maps of three-dimensional scalar fields

The paper develops an analytic method to generate inhomogeneous-resolution maps for refining atomic models in structural biology and other fields.

Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs

The paper evaluates the performance of new cryo-EM hardware for cryo-ET and subtomogram averaging using EIAV virus-like particles, showing comparable resolution and improved reconstructions with advanced processing methods.

Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

The paper presents a refinement method using HADDOCK2.4 to reduce atomic clashes in low-to-medium resolution cryo-EM complexes by optimizing protein-protein interfaces.

Cryo-ET reveals two major tubulin-based cytoskeleton structures in Toxoplasma gondii

This study uses cryo-electron tomography to reveal the molecular structures of two tubulin-based cytoskeleton structures in Toxoplasma gondii, showing their architecture and role in invasion.

UVC inactivation of pathogenic samples suitable for cryoEM analysis

This study shows that UVC irradiation at cryogenic temperatures can inactivate pathogens without damaging their structure, making them suitable for cryo-EM analysis.

3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

The paper introduces 3D-Strudel, a method for validating cryo-EM maps using resolution-dependent amino-acid motifs, and presents a visualization tool for results.

Development of a universal nanobody-binding Fab module for fiducial-assisted cryo- EM studies of membrane proteins

The paper develops a synthetic Fab module (NabFab) that binds nanobodies with high affinity, enabling high-resolution cryo-EM studies of membrane proteins.

Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering

The paper describes a platform integrating structural biology tools to rapidly determine structures of sub-100 kDa protein complexes, enabling efficient biologics discovery and engineering.

Deep Learning Improves Macromolecule Identification in 3D Cellular Cryo-Electron Tomograms

This paper introduces DeepFinder, a deep learning method that improves macromolecule identification in 3D cellular cryo-ET data by localizing multiple species with high accuracy.

Methods for analyzing continuous conformational variability of biomolecules in cryo electron subtomograms: HEMNMA-3D vs. traditional classification

The paper introduces HEMNMA-3D for analyzing continuous conformational variability in cryo-ET data and compares it to traditional methods on a simulated nucleosome dataset.

In situ imaging of bacterial membrane projections and associated protein complexes using electron cryo-tomography

The paper uses electron cryo-tomography to analyze membrane projections and associated protein complexes in bacterial species, identifying diverse structures and protein associations.

A simple pressure-assisted method for MicroED specimen preparation

This paper introduces a simple pressure-assisted method for preparing MicroED specimens, enabling control over ice thickness and handling diverse crystal samples.

Structure of the molecular bushing of the bacterial flagellar motor

The paper reports the structure of the LP ring of the bacterial flagellar motor using electron cryomicroscopy, revealing its 26-fold symmetry and intersubunit interactions.

Preparation of large-scale digitization samples for automated electron microscopy of tissue and cell ultrastructure

The paper describes a methodology for preparing large-scale digitization samples to enable automated electron microscopy, improving throughput and reducing bias in ultrastructural analysis.

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

DeepEMhancer improves cryo-EM map quality using deep learning, achieving cleaner and more detailed maps on test cases like SARS-CoV-2 RNA polymerase.

Efficient tagging and purification of endogenous proteins for structural studies by single particle cryo-EM

The paper describes a method combining CRISPR/Cas and fluorescence cell sorting to efficiently tag and purify endogenous human proteins for structural analysis using cryo-EM.

Assessment of protein-protein interfaces in cryo-EM derived assemblies

The paper introduces PI-score, a machine learning-based metric to assess protein-protein interfaces in cryo-EM-derived assemblies, identifying errors not captured by density-based methods.

VP-Detector: A 3D convolutional neural network for automated macromolecule localization and classification in cryo-electron tomograms

VP-Detector uses a 3D convolutional neural network to automatically localize and classify macromolecules in cryo-electron tomograms, achieving competitive performance with efficient processing.

DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering

DISCA uses deep learning to automatically cluster cryo-ET data into homogeneous structural subsets without templates or labels.

Permeabilization-free en bloc immunohistochemistry for correlative microscopy

This paper introduces a permeabilization-free protocol for immunohistochemistry in thick tissue sections, enabling correlative microscopy with electron microscopy and two-photon imaging.

A streamlined workflow for automated cryo focused ion beam milling

The paper introduces hardware and software improvements to enhance cryo-FIB milling for cryo-electron tomography.

Full-length de novo protein structure determination from cryo-EM maps using deep learning

This paper introduces DeepMM, a deep learning framework that automatically reconstructs full-atom protein structures from cryo-EM maps with high accuracy and coverage.

Elemental Mapping of Labeled Biological Specimens at Intermediate Energy Loss in an Energy-Filtered TEM acquired using a Direct Detection Device

The paper demonstrates improved signal-to-noise and resolution in EFTEM elemental mapping by using lower energy-loss N4,5 edges instead of core-loss M4,5 edges for lanthanide detection.

Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography

This study evaluates 15 scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography, identifying two robust methods that work across varying signal-to-noise ratios.

DRPnet - Automated Particle Picking In Cryo-Electron Micrographs Using Deep Regression

DRPnet automatically detects particle centers in cryoEM micrographs using a deep learning approach, achieving comparable or better performance than manual methods with reduced user interaction.

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning

This paper introduces DEFMap, a deep learning method that extracts dynamics information from cryo-EM maps, achieving results comparable to molecular dynamics simulations and experimental approaches.

Super-Resolution Cryo-EM Maps With 3D Deep Generative Networks

This paper introduces SuperEM, a deep learning method that improves cryo-EM map resolution, enhancing protein structure modeling.

CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks

CryoDRGN uses deep neural networks to reconstruct heterogeneous protein complexes and their motion from cryo-EM data, revealing previously unseen structural states.