AIMC Topic: Cryoelectron Microscopy

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Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM.

Nature methods Jul 29, 2021
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual macromolecules sampling different conformational and...
Humans Neural Networks, Computer Software Spike Glycoprotein, Coronavirus Protein Conformation Cryoelectron Microscopy Algorithms Deep Learning Imaging, Three-Dimensional
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Accurate prediction of protein structures and interactions using a three-track neural network.

Science (New York, N.Y.) Jul 15, 2021
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track ...
Protein Folding Sphingosine N-Acyltransferase Multiprotein Complexes Databases, Protein Protein Conformation Receptors, G-Protein-Coupled Deep Learning Protein Subunits Cryoelectron Microscopy Membrane Proteins Models, Molecular Neural Networks, Computer Proteins Amino Acid Sequence Computer Simulation ADAM Proteins Crystallography, X-Ray
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DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.

Communications biology Jul 15, 2021
Cryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on g...
Cryoelectron Microscopy Viral Proteins DNA-Directed RNA Polymerases SARS-CoV-2 Deep Learning
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Deep Learning-Based Advances in Protein Structure Prediction.

International journal of molecular sciences May 24, 2021
Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine prot...
Cryoelectron Microscopy Sequence Analysis, Protein Computational Biology Proteins Databases, Protein Models, Molecular Amino Acid Sequence Protein Conformation Software Algorithms Deep Learning Neural Networks, Computer
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Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning.

Nature communications Apr 16, 2021
An increasing number of density maps of macromolecular structures, including proteins and DNA/RNA complexes, have been determined by cryo-electron microscopy (cryo-EM). Although lately maps at a near-atomic resolution are routinely reported, there ar...
Protein Structure, Secondary Computational Biology DNA Models, Molecular RNA Nucleic Acid Conformation Cryoelectron Microscopy Software Deep Learning
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DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM.

Journal of structural biology Mar 4, 2021
Cryo Electron Microscopy (Cryo-EM) is currently one of the main tools to reveal the structural information of biological specimens at high resolution. Despite the great development of the techniques involved to solve the biological structures with Cr...
Neural Networks, Computer Deep Learning Imaging, Three-Dimensional Spike Glycoprotein, Coronavirus Plasmodium falciparum Ribosome Subunits Workflow Signal-To-Noise Ratio Cryoelectron Microscopy
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Cryo-Electron Microscopic Grid Preparation for Time-Resolved Studies using a Novel Robotic System, Spotiton.

Journal of visualized experiments : JoVE Feb 25, 2021
The capture of short-lived molecular states triggered by the early encounter of two or more interacting particles continues to be an experimental challenge of great interest to the field of cryo-electron microscopy (cryo-EM). A few methodological str...
Software Humidity User-Computer Interface Cryoelectron Microscopy Time Factors Robotics Freezing
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CASSPER is a semantic segmentation-based particle picking algorithm for single-particle cryo-electron microscopy.

Communications biology Feb 15, 2021
Particle identification and selection, which is a prerequisite for high-resolution structure determination of biological macromolecules via single-particle cryo-electron microscopy poses a major bottleneck for automating the steps of structure determ...
Cryoelectron Microscopy Humans Semantics Image Processing, Computer-Assisted Animals Proteins Deep Learning Protein Conformation Models, Molecular Single Molecule Imaging
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CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.

Nature methods Feb 4, 2021
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many imaged protein complexes exhibit conformational and compositional heterogeneity that poses a major ch...
Molecular Structure Neural Networks, Computer Macromolecular Substances Cryoelectron Microscopy
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DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM.

BMC bioinformatics Nov 9, 2020
BACKGROUND: Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the di...
Proteins Deep Learning Cluster Analysis Automation Cryoelectron Microscopy
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