Advanced Electron Microscopy Techniques and Applications

The paper introduces SPOT-RASTR, a cryo-EM technique using lipid nanotubes to overcome air-water interface and preferred orientation issues, enabling automated data collection and near-atomic resolution.

This study uses MicroED and molecular docking to determine the atomic structures and binding mechanisms of five common antidepressants from commercial powder samples.

The paper introduces a likelihood-based local docking method for cryo-EM maps, improving speed and sensitivity when component locations are known, implemented in ChimeraX.

This paper introduces EMMIVox, a Bayesian method for refining cryo-EM maps into high-quality structural models and ensembles, balancing data fit with physico-chemical accuracy.

This paper introduces a deep learning model for orientation estimation of macromolecules in cryo-ET images using synthetic data and shows promising results.

The paper introduces crefDenoiser, a self-supervised denoising model that improves the quality of 3D cryo-EM maps by amplifying signals and reducing noise.

The paper presents the cryo-EM structure of the R388 plasmid conjugative pilus, revealing a unique pilin/phospholipid complex and structural differences from other conjugative pili.

CryoJAM automates fitting homologous protein structures into medium-resolution cryo-EM density maps, reducing RMSE in most test cases.

This paper frames the challenge of interpreting cryo-EM latent spaces as an Independent Component Analysis problem, aiming to develop identifiable models for conformational landscapes.

The paper describes an automated ultra-microtome for TEM sectioning, achieving high success rates in cutting and picking up sections from various biological samples.

OPUS-TOMO improves resolution and resolves structural heterogeneity in cryo-ET data for biomolecules like ATP synthase and ribosomes.

Cryo2Struct improves de novo atomic protein structure modeling from cryo-EM density maps using a 3D transformer and HMM, outperforming Phenix on multiple metrics.

This study evaluates the Gatan Alpine detector at 100-200 keV for cryo-EM, showing improved resolution and performance compared to the Gatan K3.

The paper uses Cryo-EM to determine the structure of Aquifex aeolicus lumazine synthase at 1.42 Angstrom resolution, revealing hydrogen atoms and confirming near-atomic resolution for protein complexes.

CryoViT improves segmentation of large subcellular structures in cryoET data using vision transformers, outperforming U-Net-based methods with limited training data.

The paper develops methods to image glutamatergic synapses in hippocampal tissue using cryo-electron tomography, enabling high-resolution visualization of synaptic structures.

The paper introduces cryoSPHERE, a deep learning method for heterogeneous cryo-EM reconstruction, improving upon state-of-the-art methods in three examples.

This study uses phase plate cryo-EM to reveal conformational diversity in therapeutic IgG, achieving sub-nanometer resolution of the Fab fragment.

This study investigates factors affecting macromolecule orientations in cryo-EM thin films and identifies parameters to reduce orientation bias.

The paper reports cryoEM structures of human serum albumin with and without ligands, demonstrating the feasibility of sub-4 Å resolution mapping for proteins using standard workflows.

This paper introduces a deep-learning-based regularisation method for cryo-EM that improves reconstruction quality, enabling structure determination of smaller macromolecules with low signal-to-noise ratios.

This paper demonstrates limited-tilt serial section electron tomography for high-resolution 3D mapping of brain circuits and evaluates imaging parameters for connectomic-scale projects.

The paper introduces FilamentID, a workflow to identify filament composition in cells, finding Ald4ALDH2 and Acs1ACSS2 form filaments in mitochondria and nucleus during meiosis, aiding cell recovery from stress.

This paper demonstrates that suspended drop crystallization eliminates the missing cone challenge in MicroED for thin plate crystals.

This study uses simulations to show that frozen water cages dissociated fragments, supporting the cage effect hypothesis in cryo-EM.

Surforama enables interactive visualization and analysis of membrane proteins in cryo-ET data by rendering local densities on segmented surfaces and exporting results for further analysis.

This paper introduces a Mean Shift loss function for more accurate protein localization in cryo-electron tomography using scoremap-guided clustering and random point sampling.

The paper introduces CryoSegNet, a method combining a specialized U-Net and SAM for cryo-EM particle picking, achieving higher accuracy than existing methods.

DiffGAN estimates missing phases in single molecule cryo-electron diffraction data to determine protein structures at atomic resolution using a conditional GAN.

This paper introduces an unsupervised learning approach using coordinate networks to address the missing wedge problem in cryoET, improving reconstruction quality and reducing runtime.