{
  "schemaVersion": 1,
  "analysis": {
    "id": "structure",
    "title": "BUBR1 AlphaFold model: residues 1002, 1012 and the L737* transcript context",
    "group": "structure"
  },
  "generatedAt": "2026-10-25T04:58:34.858Z",
  "generatedBy": "BioLab Analysis Tools (www.stackfire.com)",
  "dates": {
    "archivedRecordedOn": null,
    "snapshotDataAsOf": null,
    "executions": [
      {
        "id": "structure-reproduction-check",
        "origin": "repository",
        "executedAt": "2026-09-10T11:15:52.332381+00:00",
        "recordedAt": null,
        "executionTimeSource": null,
        "timingNote": null
      }
    ],
    "note": "generatedAt is the moment this manifest was written; it is not an execution or publication date. recordedAt is packaging time; a null executedAt means the actual execution time is unknown."
  },
  "repository": {
    "sha": "a434af99342f57aa9fde958535c173b82c315c2a",
    "short": "a434af9",
    "repository": "https://github.com/ivillafuerte/mva-hackathon-2026",
    "treeUrl": "https://github.com/ivillafuerte/mva-hackathon-2026/tree/a434af99342f57aa9fde958535c173b82c315c2a"
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  "sources": [],
  "model": "A predicted model (AlphaFold), not an experimental structure. The two experimental structures checked (5KHU chain Q, 6TLJ chain S) do not cover residues 1002 or 1012.",
  "samples": "Not applicable: one predicted model of one sequence.",
  "parameters": [
    "SASA: Lee–Richards, probe 1.4 Å, 100 slices; cross-checked with Shrake–Rupley (960 points)",
    "Relative SASA with Tien 2013, Miller 1987 and FreeSASA references",
    "Rotamer grid: geometric clash search, no energies"
  ],
  "inputs": [],
  "script": null,
  "command": "python track2/structure/analyze_bubr1.py --cache data/reference/track2 --out track2/structure/results",
  "archived": null,
  "executions": [
    {
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      "executionTimeSource": null,
      "timingNote": null,
      "environment": {
        "python": null,
        "dependencies": {},
        "isolated": null,
        "pinned": null
      },
      "inputs": {
        "method": "Public reference files (AlphaFold model, PAE, UniProt entry, RefSeq transcript) verified against audited SHA-256 values.",
        "verified": 4,
        "expected": 4
      },
      "artifacts": [
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          "matches": true,
          "normalisation": null
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      ],
      "note": "Initial native runtime exited 135. Installed pinned dependencies in a clean directory using GCC; downloaded truncated public PAE reference again and verified its original hash. Final execution succeeded."
    }
  ],
  "values": [
    {
      "key": "model",
      "label": "Model",
      "value": "AF-O60566-F1-model_v6",
      "unit": "AlphaFold DB (predicted)",
      "source": {
        "label": "metrics.json (research repository)",
        "fileId": "structure-metrics"
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    },
    {
      "key": "length",
      "label": "Sequence length",
      "value": "1,050",
      "unit": "residues",
      "source": {
        "label": "metrics.json (research repository)",
        "fileId": "structure-metrics"
      }
    },
    {
      "key": "plddt1002",
      "label": "pLDDT, residue 1002 (Asn)",
      "value": "91.06",
      "unit": "model confidence",
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        "fileId": "structure-metrics"
      }
    },
    {
      "key": "sasa1002",
      "label": "SASA, residue 1002",
      "value": "27.04",
      "unit": "Ų",
      "source": {
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        "fileId": "structure-metrics"
      }
    },
    {
      "key": "rsa1002",
      "label": "Relative SASA, residue 1002 (Tien 2013)",
      "value": "13.87",
      "unit": "%",
      "source": {
        "label": "metrics.json (research repository)",
        "fileId": "structure-metrics"
      }
    },
    {
      "key": "ss1002",
      "label": "Backbone description, residue 1002",
      "value": "non-alpha/turn-or-loop; no DSSP assignment",
      "unit": "Phi/Psi proxy, not DSSP",
      "source": {
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        "fileId": "structure-metrics"
      }
    },
    {
      "key": "plddt1012",
      "label": "pLDDT, residue 1012 (Leu)",
      "value": "95.31",
      "unit": "model confidence",
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        "fileId": "structure-metrics"
      }
    },
    {
      "key": "sasa1012",
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      "unit": "Ų",
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    },
    {
      "key": "distance",
      "label": "Cα distance 1002–1012",
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      "unit": "Å",
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      }
    },
    {
      "key": "plddtWindow",
      "label": "Mean pLDDT, residues 985–1020",
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      "unit": "model confidence",
      "source": {
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        "fileId": "structure-metrics"
      }
    },
    {
      "key": "codon737",
      "label": "L737*: codon change and exon",
      "value": "TTA → TGA, exon 17, +4 base A, 73 nt to the next junction",
      "unit": "NM_001211.6",
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        "fileId": "structure-metrics"
      }
    },
    {
      "key": "codon1002",
      "label": "N1002K: codon change and exon",
      "value": "AAT → AAG, exon 23 (last exon), +4 base G",
      "unit": "NM_001211.6",
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        "fileId": "structure-metrics"
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    }
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  "crossChecks": [],
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      "id": "structure-rotamers",
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  "limitations": [],
  "whatItIsNot": "Predicted-model geometry. pLDDT is model confidence, not evidence of function; nothing here is a pathogenicity call or a drug-binding result."
}