Advanced Electron Microscopy Techniques and Applications

Molecular architecture of colossal surface layers from hyperthermophilic archaea

This study determines the structure of a large S-layer protein from Pyrobaculum arsenaticum using cryo-EM and AlphaFold, revealing its unique multidomain architecture and evolutionary conservation.

CryoForge: A Self-Correcting Agent for Cryo-EM Model Building That Learns When to Act and When to Stop

CryoForge is an evidence-gated agent that improves cryo-EM model building by selectively accepting or rejecting edits based on structural evidence, achieving validated improvements in most test cases.

Snapshots of Internal Protein Crystal Architecture at the Nanoscale

This study uses 4D-STEM to visualize nanoscale dynamics in protein microcrystals, revealing continuous rearrangements and radiolytic damage propagation.

cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle Cryo-EM

The paper introduces cFAR and Relative Signal to diagnose preferred orientation in single-particle cryo-EM, using synthetic and real datasets to validate their effectiveness.

Streamlining large-scale high-resolution electron tomography with VolWeaver

The paper optimizes a transmission electron tomography workflow for malaria parasites and introduces VolWeaver to integrate high-resolution tomographic data into serial section volume reconstructions.

Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography

The paper describes a Kaggle challenge for particle picking in cryo-electron tomography, resulting in improved algorithms and highlighting the need for better annotation quality measures.

Characterization of energy filtering slit widths for MicroED data collection

This study evaluates energy filter slit widths in MicroED to improve signal-to-noise ratio and data quality for macromolecular structure determination.

MC-Bayes: A Python-based wrapper for MotionCor3 processing of EER files compatible with Bayesian polishing

MC-Bayes provides a Python wrapper for MotionCor3 to process EER files for Bayesian polishing, enabling faster motion correction on GPU systems compared to CPU-based methods.

CryoLigATE: enhancing the resolvability of cryo-EM maps in protein-ligand complexes using deep learning

CryoLigATE improves ligand density resolution in cryo-EM maps using a deep learning framework, enhancing structural interpretation for drug discovery.

CsMT: a robust and streamlined CryoSPARC workflow for cryo-EM reconstruction of microtubules

CsMT provides a streamlined CryoSPARC workflow for cryo-EM reconstruction of microtubules, achieving high-resolution results with minimal manual intervention.

Physics-Guided Neural Reconstruction of Cellular Membranes for 3D Electron Microscopy

This paper introduces a physics-informed neural network framework to reconstruct 3D membrane shapes and curvatures from electron microscopy images, showing improved accuracy and mechanical insights.

Near-atomic in-situ architecture and membrane-coupled dynamics of the Vibrio cholerae sheathed flagellum

This study determines the near-atomic structure of Vibrio cholerae's sheathed flagellum and reveals its dynamic architecture and membrane-coupled mechanisms.

Electron counting enables cryo-electron ptychography for near-atomic-resolution cryo-electron microscopy

This paper introduces electron counting in cryo-electron ptychography to achieve near-atomic resolution for biological specimens, demonstrating 3.59 Å resolution for the T20S proteasome.

FlyTomo: A streamlined software for on-the-fly cryo-ET data processing and diagnosis

FlyTomo streamlines cryo-ET data processing and diagnosis, enabling real-time feedback and structured data management for improved structural biology research.

Streamlined Montage Cryo-Electron Tomography for Exploring the Ultrastructure of Cells and Tissues

This paper introduces a streamlined workflow for montage cryo-electron tomography that simplifies data acquisition and processing, enabling high-throughput, nanoscale-resolution imaging of biological samples.

Layered helical order reveals assembly states in podosome actin networks

The paper uses cryo-electron tomography and computational methods to infer the assembly states of actin networks in podosomes, revealing layered helical order and preferred orientation transitions.

Optimized cryo-FIB milling strategy to generate thin, minimally damaged biological lamellae

This paper introduces Nilas, a cryo-FIB milling strategy that minimizes damage and improves resolution for in situ structural biology.

DPI-score: A deep learning-based metric for assessing protein-protein interfaces in cryo-EM derived assemblies

The paper introduces DPI-Score, a deep learning metric to assess protein-protein interfaces in cryo-EM structures, showing it can detect interface errors not found by density-based scores.

Best for the Eye, Not for the Algorithm: Anisotropy in Fitting Atomic Models in Cryo-EM

The paper argues that atomic models in cryo-EM should be fitted to particle images rather than volumes, showing that weighted volumes can achieve similar results and proposing an implementation in existing software.

LowDoseWizard - rapid and standardised setup of low-dose cryo-TEM imaging in SerialEM

LowDoseWizard streamlines low-dose cryo-TEM setup in SerialEM, reducing setup time and improving reproducibility for high-resolution cryo-EM data collection.

Confidence-guided cryo-EM map optimisation with LocScale-2.0

This paper introduces LocScale-2.0 and LocScale-FEM to improve cryo-EM map quality by enhancing local detail while preserving weak structural context and providing confidence scores for interpretation.

Quinoa: Efficient and Robust CTF Estimation for CryoET Tilt Series

Quinoa provides efficient and robust CTF estimation for cryoET tilt series, improving automated structural analysis of cells and tissues.

Diversifying particle-orientation distributions in cryo-EM with LEA protein additives

This study shows that LEA proteins can reduce orientation bias and improve particle-orientation distributions in cryo-EM by mitigating air-water interface damage.

WebCalEM: a browser-based tool for routine and accurate pixel size calibration in cryo-EM

WebCalEM provides a browser-based tool for accurate pixel size calibration in cryo-EM, eliminating installation barriers and enabling routine use.

Fast prediction of acidic amino acid sidechain conformations for cryo-EM modeling

The paper develops a workflow to predict sidechain conformations of acidic amino acids in cryo-EM maps, validated through Q-score and molecular dynamics simulations.

SparseSeg: Target-Conditioned Discovery Segmentation of Cryo-Volume Electron Microscopy Under Sparse Annotation

SparseSeg improves cryo-vEM segmentation with sparse annotations by using exemplar-driven propagation and multi-kernel U-Net for accurate, context-aware organelle detection.

Narrow-beam geometry improves the efficiency of cryo-EM

This study shows that narrow-beam geometry in cryo-EM reduces radiation damage and improves signal-to-noise ratio by capturing diffraction patterns from biological specimens.

Interactive segmentation of membrane and membrane mimic densities in cryo-EM maps

The paper introduces SURFER, a tool for segmenting membrane and membrane mimic densities in cryo-EM maps to improve analysis and visualization.

CryoROLE: describing large inter-domain rotation in single particle cryo-EM

CryoROLE extracts continuous conformational dynamics from cryo-EM data by analyzing relative domain orientations, revealing hidden protein motions relevant to function.

Using spIsoNet to address the preferred-orientation problem in cryoEM reconstructions

This paper introduces spIsoNet, a deep-learning method to correct preferred-orientation bias in cryoEM reconstructions, demonstrating its effectiveness on influenza HA trimer datasets.