PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations

PHENOMS, a Rust-accelerated Python package for MD hydrogen-bond analysis, achieves an average 16-fold speedup (up to 100-fold) while preserving hydrogen-bond resolution in every trajectory frame.

• Why it matters: HDX-MS protection patterns can be hard to interpret at atomic resolution, and standard global MD metrics may miss local structural changes linked to hydrogen-bond network reorganization.
• What they did: The tool integrates molecular dynamics trajectories with HDX-MS data to track backbone hydrogen bonds and residue-residue contacts as they form, break, and reorganize across frames, using a multithreaded Rust engine.
• The result: In retrospective case studies, PHENOMS recapitulates HDX-MS protection patterns and identifies key residues driving coordinated structural changes, while also providing automated quality control and high-throughput analysis.

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