{
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    "file_name": "RosettaQ__RUN__EXP-0007-011__20260724T2201Z__ctqw-vs-diffusion--allostery-1shl-c8.5.json",
    "file_id": "EXP-0007-011",
    "type": "RUN",
    "is_demo": false,
    "scope_note": "Suite Cleveland Clinic — caspasa-3 (proteasa cisteinica; sitio alosterico de interfaz de dimero) (1SHL). Sitio alosterico = residuos que contactan el efector co-cristalizado; fuente = diada catalitica His144/Cys186 verificada por motivo QACRG (Q184-A185-C186-R187-G188) y contexto His-Gly (S143-H144-G145) + par a 4.56A. CTQW vs difusion clasica, cutoff 8.5A.",
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  "w6": {
    "que": {
      "recipe_id": "RQ-0007",
      "recipe_name": "Allosteric site identification via quantum signal propagation",
      "problem_class": "Molecular simulation / allostery",
      "instance": "1SHL_ca_cutoff8.5",
      "protein_family": "caspasa-3 (proteasa cisteinica; sitio alosterico de interfaz de dimero)",
      "quantum_side": {
        "method": "continuous-time quantum walk, U(t)=exp(-iAt), integrated",
        "allosteric_percentile": 72.7,
        "runtime_s": 2.663
      },
      "classical_side": {
        "method": "continuous-time diffusion, p(t)=exp(-Lt), integrated",
        "allosteric_percentile": 72.87,
        "runtime_s": 1.431
      },
      "ground_truth": {
        "source_active_site": [
          [
            "A",
            144
          ],
          [
            "A",
            186
          ],
          [
            "B",
            144
          ],
          [
            "B",
            186
          ]
        ],
        "allosteric_site": [
          [
            "A",
            159
          ],
          [
            "A",
            183
          ],
          [
            "A",
            213
          ],
          [
            "A",
            214
          ],
          [
            "A",
            221
          ],
          [
            "A",
            223
          ],
          [
            "A",
            290
          ],
          [
            "A",
            292
          ],
          [
            "B",
            159
          ],
          [
            "B",
            183
          ],
          [
            "B",
            213
          ],
          [
            "B",
            214
          ],
          [
            "B",
            215
          ],
          [
            "B",
            221
          ],
          [
            "B",
            223
          ],
          [
            "B",
            290
          ],
          [
            "B",
            292
          ]
        ],
        "ground_truth_method": "diada catalitica His144/Cys186 verificada por motivo QACRG (Q184-A185-C186-R187-G188) y contexto His-Gly (S143-H144-G145) + par a 4.56A; sitio alosterico = residuos <4.5A del inhibidor alosterico co-cristalizado en la cavidad de interfaz de dimero (Wells lab)",
        "n_active": 4,
        "n_allosteric": 17,
        "n_allosteric_distal": 17
      },
      "outcome": "not yet",
      "metric": "percentil medio de residuos alostericos verdaderos en el mapa de propagacion (entre residuos distales, >6A del sitio activo); 100=top",
      "scores": {
        "quantum_percentile": 72.7,
        "classical_percentile": 72.87
      }
    },
    "como": {
      "protocol": "juez-v1: misma red de residuos + mismo par fuente/tiempos; sitio alosterico definido geometricamente por el efector co-cristalizado (arbitro objetivo, ninguno de los dos lados lo define)",
      "instance_params": {
        "pdb": "1SHL",
        "cutoff_A": 8.5,
        "n_residues": 398,
        "time_window": [
          0.5,
          8.0
        ],
        "n_times": 16
      },
      "lib_versions": {
        "prody": "2.6.1",
        "numpy": "2.4.4",
        "scipy": "1.16.3",
        "python": "3.11.15"
      },
      "compute": "contenedor cloud Cowork (CPU, Linux)",
      "harness": "allo_multi.py",
      "raw_data_url": "pendiente de publicacion en repo"
    },
    "cuando": {
      "started_at": "2026-07-24T22:01:21.107904+00:00",
      "archived_at": "2026-07-24T22:01:21.107924+00:00",
      "timezone_note": "UTC; equipo en America/Punta_Arenas"
    },
    "donde": {
      "quantum_backend": "CTQW por matrix-exponential (simulacion exacta; ruta NISQ = Hamiltonian simulation gate-based)",
      "classical_backend": "difusion por matrix-exponential del Laplaciano",
      "protein_source": "RCSB PDB 1SHL via ProDy",
      "region": "cloud sandbox Anthropic"
    },
    "porque": {
      "hypothesis": "si la caminata cuantica capturara la propagacion de senal alosterica mejor que la difusion, deberia rankear el sitio alosterico verdadero mas alto de forma consistente entre familias de proteinas",
      "question": "En 1SHL (caspasa-3 (proteasa cisteinica; sitio alosterico de interfaz de dimero)), CTQW vs difusion: cual rankea mas alto el sitio alosterico definido por el efector unido?",
      "ledger_goal": "ampliar la suite RQ-0007 a mas familias con ground-truth geometrico; insumo de la propuesta Fase I Cleveland"
    },
    "quien": {
      "operator": "Nicholas",
      "agents": [
        "Claude (Cowork cloud)",
        "allo_multi.py"
      ],
      "judge_protocol_version": "juez-v1",
      "org": "Rosetta Quantum",
      "team": "Rosetta Quantum"
    }
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