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    "story_id": "mp-2026-10-20-013",
    "source_story_id": "tmp-story-proteingeobench-agent-geometry",
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    "position": 13,
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    "headline": "The Biology Agent Can Find the Protein but Misread Its Shape",
    "slug": "the-biology-agent-can-find-the-protein-but-misread-its-shape",
    "dek": "ProteinGeoBench separates metadata lookup from numerical geometry and shows how harness, access and run budget can change the ranking.",
    "summary": "ProteinGeoBench separates metadata lookup from numerical geometry and shows how harness, access and run budget can change the ranking.",
    "body_text": "Structural-biology agents are often asked to retrieve facts and compute geometry in one score. ProteinGeoBench splits those abilities across 131 tasks. In 4,249 rollouts from four frontier models, three landed within 0.031 of one another; three of the four performed better on metadata lookup than numerical calculation. Numeric questions made up 28 tasks but half of the twelve every model failed. Rankings also changed with run budget and command-line harness. The study does not crown one universal agent; it argues evaluations should expose task family, repeats, access and harness instead of letting lookup fluency hide geometric weakness.",
    "why_it_matters": "ProteinGeoBench separates metadata lookup from numerical geometry and shows how harness, access and run budget can change the ranking.",
    "limitations": [
      "The study does not crown one universal agent; it argues evaluations should expose task family, repeats, access and harness instead of letting lookup fluency hide geometric weakness."
    ],
    "importance": 8,
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    "first_published_at": "2026-10-20T09:00:00.000-04:00",
    "modified_at": "2026-10-20T09:00:00.000-04:00",
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        "text": "ProteinGeoBench separates metadata lookup from numerical geometry and shows how harness, access and run budget can change the ranking.",
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    "tags": [
      "structural biology",
      "agents",
      "evaluation"
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  "sources": [
    {
      "source_id": "source-2026-10-20-013",
      "title": "arXiv preprint 2610.26829, original v1",
      "publisher": "arXiv",
      "url": "https://arxiv.org/abs/2610.26829v1",
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      "source_type": "primary_research",
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      "published_at": "2026-10-19T13:55:38.000-04:00",
      "accessed_at": "2026-10-20T08:15:06.176-04:00",
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    "name": "The Machine Press",
    "url": "https://themachinepress.com",
    "description": "A daily newspaper for the age of artificial intelligence."
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  "cite_this_report": {
    "title": "The Biology Agent Can Find the Protein but Misread Its Shape",
    "publisher": "The Machine Press",
    "published_at": "2026-10-20T09:00:00.000-04:00",
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