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Article
Open AccessAccurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information
The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-ne...
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Article
Open AccessAccurate global and local 3D alignment of cryo-EM density maps using local spatial structural features
Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpreting...
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Article
Open AccesstrRosettaRNA: automated prediction of RNA 3D structure with transformer network
RNA 3D structure prediction is a long-standing challenge. Inspired by the recent breakthrough in protein structure prediction, we developed trRosettaRNA, an automated deep learning-based approach to RNA 3D str...
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Article
Open AccessHycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the nu...
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Chapter and Conference Paper
SaID: Simulation-Aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
Cryo-Electron Microscopy (cryo-EM) is a revolutionary technique for determining the structures of proteins and macromolecules. Physical limitations of the imaging conditions cause a very low Signal-to-Noise Ra...
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Article
Open AccessStructure of the full-length human Pannexin1 channel and insights into its role in pyroptosis
Pannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, ...
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Article
Open AccessCompressed sensing improved iterative reconstruction-reprojection algorithm for electron tomography
Electron tomography (ET) is an important technique for the study of complex biological structures and their functions. Electron tomography reconstructs the interior of a three-dimensional object from its proje...
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Chapter and Conference Paper
Dilated-DenseNet for Macromolecule Classification in Cryo-electron Tomography
Cryo-electron tomography (cryo-ET) combined with subtomogram averaging (STA) is a unique technique in revealing macromolecule structures in their near-native state. However, due to the macromolecular structura...
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Article
Open AccessPIXER: an automated particle-selection method based on segmentation using a deep neural network
Cryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, resear...
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Article
Open AccessLive cell single molecule-guided Bayesian localization super resolution microscopy
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Article
Open AccessDrift correction for single-molecule imaging by molecular constraint field, a distance minimum metric
The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with convent...