1 citations · 1 across the 7 of their papers we have counts for
7 papers
Enhancing Cryo-EM Density Map Segmentation in Phenix for Improved Atomic Model Building
Chenwei Zhang
We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation ste…
Applications of deep generative models to DNA reaction kinetics and to cryogenic electron microscopy
Chenwei Zhang
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on…
CryoSAMU: Enhancing 3D Cryo-EM Density Maps of Protein Structures at Intermediate Resolution with Structure-Aware Multimodal U-Nets
Chenwei Zhang, Khanh Dao Duc
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 Å) is crucial in protein structure determination. Recent advances in deep learning…
Struc2mapGAN: improving synthetic cryo-EM density maps with generative adversarial networks
Chenwei Zhang, Anne Condon, Khanh Dao Duc
Generating synthetic cryogenic electron microscopy 3D density maps from molecular structures has potential important applications in structural biology. Yet existing simulation-bas…
ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings
Chenwei Zhang, Jordan Lovrod, Boyan Beronov +2
Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many poten…
Visualizing DNA reaction trajectories with deep graph embedding approaches
Chenwei Zhang, Khanh Dao Duc, Anne Condon
Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts mak…
EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence
Aryan Tajmir Riahi, Chenwei Zhang, James Chen +2
Aligning EM density maps and fitting atomic models are essential steps in single particle cryogenic electron microscopy (cryo-EM), with recent methods leveraging various algorithms…