Advanced Electron Microscopy Techniques and Applications

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 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.

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

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.

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.

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.

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

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

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

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.

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

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

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.

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.

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

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.

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

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

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

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

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.

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

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

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