{
  "id": 2941671,
  "title": "Mountain Centroid: RNA Ensemble Representation with Mountain Profiles",
  "url": "https://urgent.news/2026/08/23/mountain-centroid-rna-ensemble-representation-with-mountain-profiles",
  "topic": "science",
  "section": "Science",
  "published": "2026-08-23T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.08.19.745640v1?rss=1"
  },
  "original_language": "en",
  "account": "RNA molecules often form multiple thermodynamic ensembles, necessitating a single representative structure for interpretation. Current base-pair centroid estimators evaluate agreement at the level of individual base pairs, disregarding nesting depth along the sequence. The authors present Mountain Centroid, which minimizes the expected squared mountain-profile distance and derives dynamic programming algorithms with and without RNA pairing constraints. They also integrate Mountain Centroid with the base-pair centroid gain.\n\nThe Mountain Centroid algorithm was tested against 21,254 RNAStrAlign sequences. It demonstrated a lower median normalized mean squared mountain distance (NMSMD) compared to minimum-free-energy (MFE) and base-pair centroid structures with a weight (γ) of 1. However, its median base-pair F1 score was lower. Implementing RNA pairing constraints improved base-pair F1 for 59.35% of sequences while reducing it for 3.58%. At a specific weight, the combined objective structure exhibited a median base-pair F1 score comparable to MFE while maintaining a lower median NMSMD than MFE and all tested γ-centroid settings.\n\nIn conclusion, Mountain Centroid offers a novel way to represent an RNA structural ensemble as a single secondary structure. By combining mountain-profile and individual-base-pair criteria, researchers can adjust the relative contributions of these factors to suit their needs.",
  "summary": "Background: RNA molecules form thermodynamic ensembles, but interpretation often requires a single representative structure. Existing base-pair centroid estimators assess agreement at the level of individual base pairs and do not directly target nesting depth along the sequence. Methods: We introduce Mountain Centroid, which minimizes expected squared mountain-profile distance, and derive dynamic…",
  "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."
}