Topic 111

cryo electron em structures resolution microscopy atomic determination biophysics particle structure structural crystallography maps macromolecular ray 3d method reconstruction beam images complexes refinement methods quality macromolecules atoms protein single experimental map density crystals resolutions tomography tilt software cryoem automated diffraction improve image proteins procedure approach reconstructions dimensional noise challenging microscope atom cryogenic fourier data can high collection deep particles molecular microed crystal conformational micrographs available based computationally user determining picking accurate orientations tool computational milling automatic pdb grid near three averaging processing accuracy approaches powerful building here modeling ratio improved throughput enables at determined sub relion ensembles information rosetta obtain

104 items. Top items listed below.

Breaking the next Cryo-EM resolution barrier - Atomic resolution determination of proteins! 111 51 18 8 4

Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning 111 51 26 8 4

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning 111 51 8 4

In situ structure determination using single particle cryo-electron microscopy images 111 51 18 8 4

Single-particle cryo-EM at atomic resolution 111 51 8 4

Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps 111 51 26 4

Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution 111 51 4

DeepCryoPicker: Fully Automated Deep Neural Network for Single Protein Particle Picking in cryo-EM 111 26 4

DeepTracer: Predicting Backbone Atomic Structure from High Resolution Cryo-EM Density Maps of Protein Complexes 111 105 26 4

High-resolution cryo-EM structure of photosystem II: Effects of electron beam damage 111 51 8

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.7 A inside cells 111 51 18 8 4

CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks 111 51 4

DeepTracer: Fast Cryo-EM Protein Structure Modeling and Special Studies on CoV-related Complexes 111 51 26 4

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation 111 4

Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTER 111 51 18 8 4

Routine sub-2.5 A cryo-EM structure determination of B-family G protein-coupled receptors 111 51 8 4

Improvement of cryo-EM maps by density modification 111 51 4

Data-guided Multi-Map variables for ensemble refinement of molecular movies 111 91 51 8 4

Resolving Individual-Atom of Protein Complex using Commonly Available 300-kV Cryo-electron Microscopes 111 51 8 4

A Workflow for Protein Structure Determination from Thin Crystal Lamella by Micro-Electron Diffraction 111 51 18 8 4

TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM 111 62 4

Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography 111 18 4

Sub-3 A resolution structure of apoferritin using a multi-purpose TEM with a side-entry cryo-holder 111 51 18 8 4

Improvements on marker-free images alignment for electron tomography 111 59 18 4

In situ structure determination of virus capsids imaged within cell nuclei by correlative light and cryo-electron tomography. 111 51 18 8 4

Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination 111 51 26 4

Subnanometer-resolution structure determination in situ by a hybrid subtomogram averaging - single particle cryoEM - workflow 111 51 18 4

High-resolution cryo-EM using beam-image shift at 200 keV 111 51 18 4

Enhancing SNR and generating contrast for cryo-EM images with convolutional neural networks 111 26 18 4

3D Variability Analysis: Directly resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM images 111 51 18 8 4

Topaz-Denoise: general deep denoising models for cryoEM and cryoET 111 26 4

Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data 111 105 26 4

Size matters: optimal mask diameter and box size for single-particle cryogenic electron microscopy 111 51 18 8 4

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM 111 51 26 8 4

Lattice micropatterning of electron microscopy grids for improved cellular cryo-electron tomography throughput 111 51 18 8 4

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics 111 51 8 4

Deep Learning Improves Macromolecules Localization and Identification in 3D Cellular Cryo-Electron Tomograms 111 26 4

A guided approach for subtomogram averaging of challenging macromolecular assemblies 111 51 18 4

Structure of the Bacterial Ribosome at 2 A Resolution 111 51 8 4

Automated Threshold Selection for Cryo-EM Density Maps 111 13 4

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps 111 51 13 8 4

CASSPER: A Semantic Segmentation based Particle Picking Algorithm for Single Particle Cryo-Electron Microscopy 111 26 18 4

Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography 111 4

Two particle picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER 111 26 4

Adaptive FDR thresholding of Fourier shell correlation for resolution estimation of cryo-EM maps 111 13 4

Macromolecular refinement of X-ray and cryo-electron microscopy structures with Phenix / OPLS3e for improved structure and ligand quality 111 51 4

3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy 111 18 4

Integrative Modeling of Membrane-associated Protein Assemblies 111 4

Three-dimensional reconstruction of individual helical nano-filament structures from atomic force microscopy topographs 111 18 8 4

Molecular goniometers for single-particle cryo-EM of DNA-binding proteins 111 51 8 4

Insights into actin polymerization and nucleation using a coarse grained model 111 51 8

Generation of ordered protein assemblies using rigid three-body fusion 111 51 8 4

Real-space quantum-based refinement for cryo-EM: Q|R#3 111 51 4

A Robust Method for Collecting X-ray Diffraction Data from Protein Crystals across Physiological Temperatures 111 8 4

Automatic de novo atomic-accuracy structure determination for cryo-EM maps using deep learning 111 26 4

Determining structures of biomacromolecular complexes from ambiguous NMR restraints and cryoEM data 111 18 4

Local computational methods to improve the interpretability and analysis of cryo-EM maps 111 51 18 4

MicroED structure of lipid-embedded mammalian mitochondrial voltage dependent anion channel 111 8

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing 111 26 4

FSC-Q: A CryoEM map-to-atomic model quality validation based on the local Fourier Shell Correlation 111 59 4

Automated and statistically corrected identification of flexible multivalent IDP-bound assemblies in electron micrographs 111 8 4

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution 111 59 4

Amorphous nickel titanium alloy film: a new choice for cryo electron microscopy sample preparation 111 51 18 8

CryoGAN: A New Reconstruction Paradigm for Single-particle Cryo-EM Via Deep Adversarial Learning 111 26 4

Visual Biochemistry: modular microfluidics enables kinetic insight from time-resolved cryo-EM 111 18 8 4

Specificities of modeling membrane proteins using multi-template homology modeling 111 51 4

Statistics and classification of spatial rotations and projection directions considering molecular symmetry in 3D electron cryo-microscopy 111 18 4

A streamlined workflow for automated cryo focused ion beam milling 195 111 18 4

Density modification of cryo-EM maps 111 83 38 4

Serial protein crystallography in an electron microscope 111 18 8

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion 103 1

Statistically correcting dynamical electron scattering improves refinement of protein nanocrystals, including charge refinement of coordinated metals 7 4

3D Deconvolution Processing for STEM Cryo-Tomography 70 18 8 4

Quantitative method for estimating stain density in electron microscopy of conventionally prepared biological specimens 111 18 4

Real time structural search of the Protein Data Bank 140 111 4

Direct label-free imaging of nanodomains in biomimetic and biological membranes by cryogenic electron microscopy 78 51 8

Fourier shell correlation criteria for local resolution estimation 111 59 18 4

Learned SPARCOM: Unfolded Deep Super-Resolution Microscopy 184 70 26 18 4

EM-net: Deep learning for electron microscopy image segmentation 26 4

A Self-Supervised Workflow for Particle Picking in Cryo-EM 111 26 4

Statistics of spatial rotations in 3D electron cryo-microscopy by unit quaternion description 111 18 4

Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures 111 7

MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP 111 8

Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography 59 4

Improved protein structure refinement guided by deep learning based accuracy estimation 105 26 4

CorRelator: An interactive and flexible toolkit for high-precision cryo-correlative light and electron microscopy 62 13 4

A common problem in the purification of calicivirus raised by molecular sieving: balance between purification and loss of viral particles 111 18

Structures, conformations and distributions of SARS-CoV-2 spike protein trimers on intact virions 36 1

Visualizing drug inhibitor binding interactions using microcrystal electron diffraction 111 8

Leveraging non-structural data to predict structures of protein-ligand complexes 105 26 4

Efficient, high-throughput ligand incorporation into protein microcrystals by on-grid soaking 111 63 8

Defocus-dependent Thon-ring fading 111 18 8

High-Resolution Single-Molecule FRET via DNA eXchange (FRET X) 111 18 8 4

Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins 184 105 13 4

Computational Tool for Ensemble Averaging of Single-Molecule Data 62 18 4

Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy 70 18 4

On the functional annotation of open-channel structures in the glycine receptor 51 8

Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement 111 91 63 8 4

EM-stellar: benchmarking deep learning for electron microscopy image segmentation 26 4

Precision design of single and multi-heme de novo proteins 111 63 8