{
  "run_id": "phase1-no-fixture-manual-simplefold-reader-2026-05-14-v2",
  "paper_doi": "10.48550/arXiv.2509.18480",
  "paper_title": "SimpleFold: Folding Proteins is Simpler than You Think",
  "model_name": "simplefold-3b",
  "apple_silicon_path": "native_mlx",
  "recipe": {
    "paper_doi": "10.48550/arXiv.2509.18480",
    "paper_title": "SimpleFold: Folding Proteins is Simpler than You Think",
    "paper_year": 2025,
    "headline_metric": {
      "name": "CASP14 SimpleFold-3B median LDDT",
      "value": 0.709,
      "tolerance_pct": 10,
      "units": "LDDT"
    },
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      "PDB experimental data",
      "AFDB SwissProt",
      "AFESM",
      "AFESM-E",
      "CAMEO22",
      "CASP14"
    ],
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      {
        "name": "SimpleFold-3B",
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      "T1093",
      "T1094",
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    "evaluation_metric": "LDDT",
    "quotes": [
      {
        "field": "paper_title",
        "text": "SimpleFold: Folding Proteins is Simpler than You Think",
        "page": 1
      },
      {
        "field": "paper_doi",
        "text": "https://doi.org/10.48550/arXiv.2509.18480",
        "page": 1
      },
      {
        "field": "models.name",
        "text": "We scale SimpleFold to 3B parameters",
        "page": 1
      },
      {
        "field": "models.code_url",
        "text": "Code: https://github.com/apple/ml-simplefold",
        "page": 1
      },
      {
        "field": "models.apple_silicon_path",
        "text": "Due to its general-purpose architecture, SimpleFold shows efficiency in deployment and inference on consumer-level hardware.",
        "page": 1
      },
      {
        "field": "models.apple_silicon_path",
        "text": "We provide support for both PyTorch and MLX (recommended for Apple hardware) backends in inference.",
        "page": 0
      },
      {
        "field": "data_sources",
        "text": "We train SimpleFold with a data mix of 3 different sources.",
        "page": 6
      },
      {
        "field": "data_sources",
        "text": "we train our largest SimpleFold-3B on the distilled AFESM-E data together with PDB and SwissProt.",
        "page": 6
      },
      {
        "field": "evaluation_set",
        "text": "We evaluate SimpleFold on two widely adopted protein structure prediction benchmarks: CAMEO22 and CASP14",
        "page": 8
      },
      {
        "field": "evaluation_set",
        "text": "List of 70 targets in CASP14",
        "page": 24
      },
      {
        "field": "evaluation_metric",
        "text": "We report standard structure prediction metrics: TM-score and GDT-TS assess global structural similarity; LDDT and LDDT-Ca measure local atomic accuracy",
        "page": 8
      },
      {
        "field": "headline_metric",
        "text": "SimpleFold-3B                      0.720 / 0.792   0.639 / 0.703   0.666 / 0.709",
        "page": 9
      },
      {
        "field": "manual_curation_status",
        "text": "MANUAL_CURATED_READER_OUTPUT: produced by pilot/local-runner/scripts/manual-simplefold-reader.mjs from primary arXiv PDF text plus official Apple repository README; use until command-agent credentials are available.",
        "page": 0
      }
    ]
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}