Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the
determination of high-resolution 3-Dimensional (3D) structures of large biological …
determination of high-resolution 3-Dimensional (3D) structures of large biological …
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM
Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-
EM-based protein structure determination. Converting density maps into 3D atomic …
EM-based protein structure determination. Converting density maps into 3D atomic …
Cryo-EM: A window into the dynamic world of RNA molecules
X Zhang, S Li, K Zhang - Current Opinion in Structural Biology, 2024 - Elsevier
RNAs are critical for complex cellular functions, characterized by their structural versatility
and ability to undergo conformational transitions in response to cellular cues. The elusive …
and ability to undergo conformational transitions in response to cellular cues. The elusive …
Accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net
Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step
in the cryo-EM-based structure determination. However, existing methods trained on a …
in the cryo-EM-based structure determination. However, existing methods trained on a …
[HTML][HTML] CryoVirusDB: a labeled cryo-EM image dataset for AI-driven virus particle picking
With the advancements in instrumentation, image processing algorithms, and computational
capabilities, single-particle electron cryo-microscopy (cryo-EM) has achieved nearly atomic …
capabilities, single-particle electron cryo-microscopy (cryo-EM) has achieved nearly atomic …
AI-based methods for biomolecular structure modeling for Cryo-EM
Highlights•Cryo-EM structure determination involves numerous computational data
processing steps.•Many AI-based methods have been developed for cryo-EM data …
processing steps.•Many AI-based methods have been developed for cryo-EM data …
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net
Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step
in the cryo-EM-based structure determination. However, existing methods trained on a …
in the cryo-EM-based structure determination. However, existing methods trained on a …
Ligand identification in CryoEM and X-ray maps using deep learning
J Karolczak, A Przybyłowska, K Szewczyk… - …, 2025 - academic.oup.com
Motivation Accurately identifying ligands plays a crucial role in the process of structure-
guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample …
guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample …
UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs
C Zhang, Y Cheng, K Feng, F Zhang… - Briefings in …, 2025 - academic.oup.com
Automatic single particle picking is a critical step in the data processing pipeline of cryo-
electron microscopy structure reconstruction. In recent years, several deep learning-based …
electron microscopy structure reconstruction. In recent years, several deep learning-based …
Transformer in Microbial Image Analysis: A Comparative Exploration of TransUNet, UNet, and DoubleUNet for SEM Image Segmentation
BDS Gurung, A Khanal, TW Hartman… - 2023 IEEE …, 2023 - ieeexplore.ieee.org
The advent of transformer-based architectures such as TransUNet has revolutionized image
segmentation as this approach combines the strengths of transformers for capturing …
segmentation as this approach combines the strengths of transformers for capturing …