{
  "id": 17303955,
  "title": "PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations",
  "url": "https://urgent.news/2026/10/30/phenoms-open-source-software-for-rust-accelerated-hydrogen-bond",
  "topic": "finance",
  "section": "Finance & Markets",
  "published": "2026-10-30T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.10.26.761768v1?rss=1"
  },
  "original_language": "en",
  "account": "Hydrogen-deuterium exchange mass spectrometry (HDX-MS) offers valuable insights into protein structure and dynamics, but deciphering protection patterns at the atomic level typically necessitates supplementary computational modeling. The authors introduce PHENOMS, an open-source Python package designed to merge molecular dynamics trajectories with HDX-MS data, facilitating the examination of backbone hydrogen-bond networks by monitoring the formation, dissolution, and reorganization of individual hydrogen bonds and residue-residue contacts throughout simulations. This residue-level analysis can unveil subtle local structural alterations that might be overlooked by traditional global trajectory metrics.\n\nTo enhance computational efficiency, PHENOMS leverages a multithreaded, Rust-accelerated computational engine. Benchmarking against other widely-used Python-based MD analysis packages revealed that PHENOMS achieved an average 16-fold speedup (potentially reaching 100-fold), all while preserving individual hydrogen-bond resolution in every trajectory frame. The authors validated PHENOMS through several retrospective case studies utilizing both published and in-house datasets. Their findings demonstrated that PHENOMS could accurately replicate HDX-MS protection patterns, pinpoint critical residues driving coordinated structural changes, and evaluate the computational efficiency of the approach.\n\nWith integrated quality-control workflows, PHENOMS offers a comprehensive framework for combining hydrogen-bond analysis with HDX-MS data or serves as a standalone, high-throughput tool for scrutinizing MD trajectories, finding utility in various domains such as protein engineering, drug discovery, and structural biology.",
  "summary": "Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides powerful insight into protein structure and dynamics, but interpretation of protection patterns at atomic resolution often requires complementary computational modeling. We present PHENOMS, an open-source Python package that integrates molecular dynamics trajectories with HDX-MS data to analyze backbone hydrogen-bond networks by…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 1,
    "also_reported_by": []
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}