#36 · Structural bio & protein design

Computational pipelines for cryo-EM reconstruction and ligand-density analysis

The dominant thread is the move from manual, sequential structure workflows toward automated, density-aware computation. CryoPilot uses two LLM agents to select CryoSPARC jobs adaptively and validate atomic models across nine public datasets. End2EndPtychoSPA instead fits a 3D potential and particle poses jointly to 4D-STEM data through a differentiable multislice model, reporting resolution gains over sequential reconstruction. On the hit-identification side, FoXSight applies Difference-of-Gaussian filtering to multi-reference subtraction maps to recover recurring ligand-bound density in crystallographic fragment screens, while Astex-Faro flags significant deviations in cryo-EM maps against a reference ensemble and introduces an FSCoh consistency metric. PHENOMS addresses a separate analysis problem, Rust-accelerated extraction of backbone hydrogen-bond networks from MD trajectories linked to HDX-MS.