{
  "comparison": "Cross-Model MCL-1 Co-Fold Verification",
  "target": "MCL-1 (Myeloid Cell Leukemia 1)",
  "experimental_pdb": "5FDR",
  "verification_engine": "SIGMA (Sheaf-based Structural Verification)",
  "parameters_learned": 0,
  "gpu_required": false,
  "modes_comparable": false,
  "models": {
    "OpenFold3": {
      "release_date": "2024",
      "organization": "OpenFold Consortium",
      "summary": {
        "model": "OpenFold3",
        "output_mode": "protein_ligand_complex",
        "interface_tested": true,
        "n_samples": 5,
        "backbone_mean": 0.9772,
        "steric_mean": 1.0,
        "h1_mean": 0.8,
        "h1_zero_count": 1,
        "obs_mean": 19.8,
        "verdicts": {
          "PASS": 5
        },
        "cofold_mean": 0.951,
        "cofold_min": 0.9195,
        "cofold_max": 0.9786,
        "cofold_range": 0.0591,
        "iface_suf_mean": 0.9773,
        "iface_geo_mean": 0.9035,
        "best_cofold_sample": 4
      }
    },
    "ESMFold2": {
      "release_date": "2026-05-27",
      "organization": "Biohub",
      "summary": {
        "model": "ESMFold2",
        "output_mode": "monomer_or_protein_only",
        "interface_tested": false,
        "n_samples": 1,
        "backbone_mean": 0.9364,
        "steric_mean": 1.0,
        "h1_mean": 0.0,
        "h1_zero_count": 1,
        "obs_mean": 11.0,
        "verdicts": {
          "PASS": 1
        },
        "cofold_mean": null,
        "cofold_note": "NOT_COMPARABLE (monomer-only, no ligand)",
        "iface_suf_mean": null,
        "iface_suf_note": "NOT_COMPARABLE (no interface tested)",
        "iface_geo_mean": null,
        "iface_geo_note": "NOT_COMPARABLE (no interface tested)",
        "best_backbone_sample": 1
      }
    }
  },
  "obstruction_overlap": {
    "shared": [],
    "of3_only": [
      "AALA58",
      "AARG15",
      "AARG32",
      "AARG53",
      "AASN113",
      "AASN54",
      "AASN91",
      "AASP154",
      "AASP2",
      "AASP26",
      "AASP3",
      "AGLN20",
      "AGLU153",
      "AGLU156",
      "AGLU19",
      "AGLY142",
      "AGLY157",
      "AGLY23",
      "AGLY34",
      "ALYS69",
      "ALYS75",
      "ASER33",
      "ASER76",
      "ATHR22",
      "ATHR27",
      "ATHR90",
      "ATRP143",
      "ATYR16",
      "AVAL152",
      "BASN70",
      "BGLN20",
      "BGLU19",
      "BLYS69"
    ],
    "esm_only": [
      "AALA28",
      "AALA37",
      "AALA53",
      "AARG34",
      "ACYS16",
      "AGLU39",
      "AGLU52",
      "AGLY17",
      "AGLY27",
      "AGLY51",
      "ALEU35",
      "ATHR29",
      "AVAL9"
    ]
  },
  "obstruction_overlap_caveat": "Obstruction sets are asymmetric; read as a first-look observation, not a benchmark. OpenFold3's set is a union across 5 sample(s) of a protein-ligand complex; ESMFold2's is from 1 monomer sample(s) (chain A only). A multi-sample union spans more residues than a single sample. 4 OpenFold3 obstruction residues are on chain B (BASN70, BGLN20, BGLU19, BLYS69) and cannot overlap a chain-A-only monomer by construction.",
  "comparison_rules": {
    "cofold_comparable": false,
    "rule": "CoFold quality compared only when both models output protein-ligand complexes. For monomer-only outputs, backbone, steric, H^1, and obstruction metrics are used. Interface scores marked NOT_COMPARABLE when no ligand is present."
  },
  "key_findings": [
    "Output modes differ: OpenFold3 produces protein_ligand_complex, ESMFold2 produces monomer_or_protein_only. CoFold quality is not directly comparable.",
    "OpenFold3 has higher mean backbone quality (0.9772 vs 0.9364).",
    "Zero shared obstruction residues, but the comparison is asymmetric (multi-sample complex union vs single monomer); see obstruction_overlap_caveat."
  ]
}