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q-bio.BM2026
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…
q-bio.BM2023
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…
q-bio.BM2023★ 1 cited
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…