{
  "id": 1737350,
  "title": "Resolution-standardized evaluation of ligand atomic coordinates in crystallographic structures using machine learning",
  "url": "https://urgent.news/2026/08/18/resolution-standardized-evaluation-of-ligand-atomic-coordinates-in",
  "topic": "ai",
  "section": "AI",
  "published": "2026-08-18T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.08.17.745351v1?rss=1"
  },
  "original_language": "en",
  "account": "Accurate evaluation of ligand coordinate-density consistency across varying resolutions has long been a challenge in macromolecular crystallography. To address this issue, the authors have introduced the atomic Box Correlation Coefficient (aBCC), an atom-level metric designed to assess the consistency between ligand atomic coordinates and electron density within a resolution-standardized framework. The development of QAEmap, a machine learning model based on three-dimensional convolutional neural networks (3D-CNNs), enabled the prediction of aBCC values from electron-density maps. Trained using Fourier-truncated electron-density maps and ligand coordinates generated from high-resolution structures in the Protein Data Bank, QAEmap was evaluated using both truncated electron-density maps and experimentally determined PDB structures. The results showed that while the prediction accuracy of aBCC gradually decreased with decreasing resolution, it remained reliable up to a resolution of approximately 3.5 angstrom. These findings demonstrate that aBCC provides a valuable tool for resolution-standardized atom-wise evaluation of coordinate-density consistency across various resolutions, laying the groundwork for further advancements and refinements in machine learning-based coordinate validation techniques.",
  "summary": "Accurate assessment of ligand coordinate-density consistency across different resolutions remains challenging in macromolecular crystallography. We introduce the atomic Box Correlation Coefficient (aBCC), an atom-level metric for evaluating the consistency between ligand atomic coordinates and electron density in a resolution-standardized framework. To predict aBCC values from electron-density…",
  "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."
}