AIMC Topic: Cryoelectron Microscopy

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Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins.

Nature communications Jul 9, 2025
Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode trans...
Iron Hemoglobins Escherichia coli Models, Molecular Crystallography, X-Ray Bacterial Outer Membrane Proteins Cryoelectron Microscopy Heme Escherichia coli Proteins Protein Binding
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MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.

Nature communications Jul 4, 2025
At sufficiently high resolution, x-ray crystallography and cryogenic electron microscopy are capable of resolving small spherical map features corresponding to either water or ions. Correct classification of these sites provides crucial insight for u...
Ions Proteins Crystallography, X-Ray Models, Molecular Deep Learning Cryoelectron Microscopy Water
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Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference.

Proceedings of the National Academy of Sciences of the United States of America Jun 4, 2025
Characterizing the conformational ensemble of biomolecular systems is key to understand their functions. Cryoelectron microscopy (cryo-EM) captures two-dimensional snapshots of biomolecular ensembles, giving in principle access to thermodynamics. How...
Models, Molecular Bayes Theorem Molecular Conformation Cryoelectron Microscopy Deep Learning Image Processing, Computer-Assisted Neural Networks, Computer Computer Simulation
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Advancing Molecular Simulations: Merging Physical Models, Experiments, and AI to Tackle Multiscale Complexity.

The journal of physical chemistry letters Apr 3, 2025
Proteins and protein complexes form adaptable networks that regulate essential biochemical pathways and define cell phenotypes through dynamic mechanisms and interactions. Advances in structural biology and molecular simulations have revealed how pro...
Proteins Molecular Dynamics Simulation Machine Learning Protein Conformation Cryoelectron Microscopy
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A review of denoising methods in single-particle cryo-EM.

Micron (Oxford, England : 1993) Mar 29, 2025
Cryo-EM has become a vital technique for resolving macromolecular structures at near-atomic resolution, enabling the visualization of proteins and large molecular complexes. However, the images are often accompanied by extremely low SNR, which poses ...
Image Processing, Computer-Assisted Proteins Deep Learning Imaging, Three-Dimensional Single Molecule Imaging Cryoelectron Microscopy Macromolecular Substances Signal-To-Noise Ratio
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Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization.

Journal of chemical information and modeling Mar 28, 2025
With the breakthroughs in protein structure prediction technology, constructing atomic structures from cryo-electron microscopy (cryo-EM) density maps through structural fitting has become increasingly critical. However, the accuracy of the construct...
Deep Learning Proteins Cryoelectron Microscopy Models, Molecular Protein Conformation
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FakET: Simulating cryo-electron tomograms with neural style transfer.

Structure (London, England : 1993) Feb 12, 2025
In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often emplo...
Software Electron Microscope Tomography Algorithms Image Processing, Computer-Assisted Deep Learning Cryoelectron Microscopy
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Advancing structure modeling from cryo-EM maps with deep learning.

Biochemical Society transactions Feb 7, 2025
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of biomolecular structures that are challenging to resolve using conventional methods. Interpreting a cryo-EM map requires accurate modeling of the...
Protein Conformation Cryoelectron Microscopy Proteins Models, Molecular Deep Learning
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AI-based methods for biomolecular structure modeling for Cryo-EM.

Current opinion in structural biology Jan 27, 2025
Cryo-electron microscopy (Cryo-EM) has revolutionized structural biology by enabling the determination of macromolecular structures that were challenging to study with conventional methods. Processing cryo-EM data involves several computational steps...
Cryoelectron Microscopy Models, Molecular Artificial Intelligence Macromolecular Substances Deep Learning
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Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning.

Journal of chemical information and modeling Jan 21, 2025
With the resolution revolution of cryo-electron microscopy (cryo-EM) and the rapid development of image processing technology, cryo-EM has become an indispensable experimental method for determining the three-dimensional structures of biological macr...
Protein Structure, Secondary Deep Learning Nucleic Acids Proteins Cryoelectron Microscopy Models, Molecular
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