{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@type": "CreativeWork",
      "@id": "ro-crate-metadata.json",
      "conformsTo": {
        "@id": "https://w3id.org/ro/crate/1.1"
      },
      "about": {
        "@id": "./"
      }
    },
    {
      "@type": "Dataset",
      "@id": "./",
      "name": "E-DICE-R Research Object \u2014 RO-PPP3CC",
      "identifier": "RO-PPP3CC",
      "datePublished": "2026-09-27T05:04:41.423497+00:00",
      "engine": "E-DICE-Core",
      "engineVersion": "0.1.0",
      "nsfTag": "NSF-EDICE-PHASE-I",
      "integrityHash": "5af465b75ca75a71",
      "hasPart": [
        {
          "@id": "#result"
        },
        {
          "@id": "#admissibility-evidence"
        },
        {
          "@id": "#trust"
        },
        {
          "@id": "#targets"
        },
        {
          "@id": "#billing"
        },
        {
          "@id": "#evidence-chain"
        },
        {
          "@id": "#performance"
        }
      ]
    },
    {
      "@type": "ComputationalResult",
      "@id": "#result",
      "name": "GPU Docking Result",
      "description": "De novo molecules generated and docked against PPP3CC via smina on g4dn.xlarge.",
      "target": "PPP3CC",
      "action": "gpu_docking",
      "totalCompounds": 32,
      "bestVina": -9.0,
      "bestSMILES": "O=C(Nc1ccc2ncccc2c1)c1ccc(F)c(NC(=O)C2CC2)c1",
      "qed": "0.748",
      "mw": "349.4",
      "substrate": "gpu",
      "decision": "DOCKED",
      "top5": [
        {
          "rank": 1,
          "smiles": "O=C(Nc1ccc2ncccc2c1)c1ccc(F)c(NC(=O)C2CC2)c1",
          "vina": -9.0
        },
        {
          "rank": 2,
          "smiles": "O=C(NCc1ccc2[nH]ccc2c1)c1cc2ccccc2[nH]1",
          "vina": -8.7
        },
        {
          "rank": 3,
          "smiles": "NS(=O)(=O)c1ccc(CNC(=O)c2cc3ccccc3[nH]2)cc1",
          "vina": -8.7
        },
        {
          "rank": 4,
          "smiles": "O=C(NCc1ccc(C(F)(F)F)cc1)c1cc2ccccc2[nH]1",
          "vina": -8.6
        },
        {
          "rank": 5,
          "smiles": "O=C(Nc1nc(-c2ccccc2)cs1)c1ccccc1",
          "vina": -8.2
        }
      ]
    },
    {
      "@type": "AdmissibilityEvidence",
      "@id": "#admissibility-evidence",
      "name": "Four-Metric Admissibility Gate",
      "nimScore": 0.75,
      "criticConfidence": 0.85,
      "thresholds": {
        "S": 0.75,
        "sigma_sq": 0.5,
        "R_theta": 0.05,
        "R_h": 2.0
      },
      "gateType": "all-or-nothing",
      "note": "All four metrics must independently pass."
    },
    {
      "@type": "GovernanceTrust",
      "@id": "#trust",
      "name": "Governance Chain",
      "pqmStatus": "ISSUED",
      "qcmTrust": 1.0,
      "qdmSubstrate": "gpu",
      "parityStatus": "VALIDATED",
      "ledgerLogged": true,
      "ledgerHash": "5af465b75ca75a71",
      "roCrateUri": "s3://edicer-dev-research-objects-865950114883/ro-crates/RO-PPP3CC/ro-crate-metadata.json"
    },
    {
      "@type": "TargetPanel",
      "@id": "#targets",
      "name": "Multi-Target Docking Panel",
      "primaryTarget": "PPP3CC",
      "totalTargetsHit": 0,
      "targets": [],
      "note": "Populated at query time with all targets sharing this compound."
    },
    {
      "@type": "BillingRecord",
      "@id": "#billing",
      "name": "Compute Cost Ledger",
      "data": {
        "total_cost": "0.72",
        "updated": "2026-05-26T16:21:18.115075+00:00",
        "data": "{\"gene\": \"PPP3CC\", \"internal_cost_usd\": \"0.72\", \"retail_price_usd\": \"650.00\", \"margin_pct\": \"99.9\", \"pharma_benchmark_usd\": \"10000000\", \"cost_reduction_vs_pharma\": \"15384\", \"cost_reduction_vs_internal\": \"13888888\", \"services\": {\"discovery_scan\": {\"description\": \"Lambda + DynamoDB\", \"duration_sec\": 30, \"internal_usd\": \"0.05\", \"retail_usd\": \"50.00\"}, \"pre_filters\": {\"description\": \"Lambda (GTEx/UniProt/OpenTargets API)\", \"duration_sec\": 15, \"internal_usd\": \"0.02\", \"retail_usd\": \"25.00\"}, \"pdb_retrieval\": {\"description\": \"AlphaFold API + S3\", \"duration_sec\": 5, \"internal_usd\": \"0.01\", \"retail_usd\": \"10.00\"}, \"denovo_generation\": {\"description\": \"Lambda (RDKit/SELFIES)\", \"duration_sec\": 60, \"internal_usd\": \"0.08\", \"retail_usd\": \"75.00\"}, \"gpu_docking\": {\"description\": \"AWS Batch g4dn.xlarge (smina)\", \"duration_sec\": 600, \"internal_usd\": \"0.53\", \"retail_usd\": \"350.00\"}, \"scoring\": {\"description\": \"Lambda (5-dim scorer)\", \"duration_sec\": 5, \"internal_usd\": \"0.01\", \"retail_usd\": \"40.00\"}, \"ro_crate\": {\"description\": \"Lambda + S3 (RO-Crate + Object Lock)\", \"duration_sec\": 3, \"internal_usd\": \"0.01\", \"retail_usd\": \"50.00\"}, \"evidence_chain\": {\"description\": \"DynamoDB + S3 immutable ledger\", \"duration_sec\": 2, \"internal_usd\": \"0.01\", \"retail_usd\": \"50.00\"}}, \"compute_type\": \"gpu\", \"instance\": \"g4dn.xlarge\", \"timestamp\": \"2026-05-26T16:21:18.115075+00:00\"}",
        "retail_price": "650.00"
      }
    },
    {
      "@type": "EvidenceChain",
      "@id": "#evidence-chain",
      "name": "Pipeline Evidence Chain",
      "stepsComplete": 9,
      "steps": {
        "prior_evidence": [
          {
            "candidates_docked": 0,
            "candidates_generated": 1,
            "decided_by": "gpu-batch-rs (autonomous pipeline)",
            "decision": "FAILED_NO_VIABLE_COMPOUNDS",
            "job_id": "ef702809-30d3-4023-b6b9-77d07d32016f",
            "next_step": "Redock with expanded scaffold library",
            "reason": "All generated de novo compounds rejected by G4-G5 quality gates (pose variance or vina threshold)",
            "step_0_provenance": {
              "approved_at": "",
              "approved_by": "auto_approved",
              "compute_type": "GPU docking (GNINA + Uni-Dock)",
              "initiated_by": "platform",
              "job_definition": "cortex-docking-gpu",
              "job_id": "60d51241-67ec-42f4-bc66-32f27541d7b3",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00"
            },
            "step_3_bio_validation": {
              "corrected_vina": -4.5,
              "correction_method": "No correction needed (experimental structure, soluble) + RotBond penalty +3.0 (12 bonds)",
              "flags": [],
              "gates_passed": 4,
              "gates_total": 4,
              "original_vina": -7.5406,
              "source": "Biological Validation Gate",
              "status": "PASS",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00",
              "trust_level": "MEDIUM"
            },
            "step_4_gpu_docking": {
              "job_id": "60d51241-67ec-42f4-bc66-32f27541d7b3",
              "n_molecules": 6,
              "n_poses": 2,
              "pose_variance": 0.849,
              "source": "GPU Docking Worker (Uni-Dock) [Rust]",
              "status": "COMPLETE",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00",
              "vina_score": -7.5406
            },
            "step_5_scoring": {
              "affinity_band": "B+",
              "cap_reason": "Cortex upgraded: B \u2192 A (BioBrain=0.62, vina suggested B)",
              "grade": "A",
              "next_action": "Medicinal chemistry optimization \u2192 improve QED above 0.5",
              "source": "5-Dimension Scorer (Rust inline) v6",
              "status": "COMPLETE",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00",
              "total_score": 0.5654,
              "vina_score": -7.5406
            },
            "step_6_billing": {
              "internal_cost_usd": "0.21",
              "retail_price_usd": "650.00",
              "source": "Governed Billing Ledger",
              "status": "COMPLETE",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00"
            },
            "step_8_npead": {
              "chemistry_score": 1.0,
              "grade_logged": "A",
              "is_membrane": false,
              "outcome_fed_to_maml": true,
              "pose_variance": 0.849,
              "source": "NPEAD Learning System",
              "status": "LOGGED",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00",
              "vina_logged": -7.5406
            },
            "step_9_intelligence": {
              "brain_bus_consulted": true,
              "cross_target_patterns": true,
              "failure_taxonomy_checked": true,
              "learned_knowledge_consulted": true,
              "smos_memories_queried": true,
              "source": "Cortex Intelligence Layer",
              "status": "COMPLETE",
              "timestamp": "2026-06-19T19:32:27.792504896+00:00"
            },
            "step_master_brain": {
              "action": "generate",
              "chosen_by": "",
              "consensus": {
                "arbitration": "",
                "llm_said": "",
                "rule_said": ""
              },
              "context": {
                "authority": 0.5,
                "failures": 0,
                "inhibitors": 8,
                "runs": 1
              },
              "directives": {
                "explore_ratio": 0.5,
                "focus": "balanced",
                "scaffold_hint": "",
                "weight_overrides": {}
              },
              "method": "rules_only",
              "rationale": "Standard generation \u2014 no signals require special handling",
              "risk": "",
              "timestamp": "2026-06-29T21:01:12.210598Z"
            },
            "timestamp": "2026-06-13T11:32:04.640026409+00:00"
          },
          {
            "compound_smiles": "O=C(Nc1ccc2ncccc2c1)c1ccc(F)c(NC(=O)C2CC2)c1",
            "estimated_cost": "$22,000\u2013$36,000",
            "gene": "PPP3CC",
            "grade": "A",
            "hash": "bc9dd75022aec784b986fce403dc0f8c2a6784cdfc09eb0a0f786e57323f5a94",
            "order_id": "WL-PPP3CC-20260630",
            "step": "wetlab_order_generated",
            "timeline": "6\u201310 weeks",
            "timestamp": "2026-06-30T15:09:41.187570+00:00",
            "trust_level": "HIGH",
            "vina_score": "-9.0"
          }
        ],
        "step_0_provenance": {
          "approved_at": "",
          "approved_by": "auto_approved",
          "compute_type": "GPU docking (GNINA + Uni-Dock)",
          "initiated_by": "platform",
          "job_definition": "cortex-docking-gpu",
          "job_id": "e50a79c0-cf78-4da0-86b4-52ee17b79a90",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00"
        },
        "step_3_bio_validation": {
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          "correction_method": "No correction needed (experimental structure, soluble)",
          "flags": [],
          "gates_passed": 4,
          "gates_total": 4,
          "original_vina": -8.1106,
          "source": "Biological Validation Gate",
          "status": "PASS",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00",
          "trust_level": "HIGH"
        },
        "step_4_gpu_docking": {
          "job_id": "e50a79c0-cf78-4da0-86b4-52ee17b79a90",
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          "n_poses": 1,
          "pose_variance": 0.0,
          "source": "GPU Docking Worker (Uni-Dock) [Rust]",
          "status": "COMPLETE",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00",
          "vina_score": -8.1106
        },
        "step_5_scoring": {
          "affinity_band": "A",
          "cap_reason": "Cortex upgraded: B+ \u2192 A+ (BioBrain=0.75, vina suggested B+)",
          "grade": "A+",
          "next_action": "Generate diverse analogs \u2192 re-dock best \u2192 target A grade",
          "source": "5-Dimension Scorer (Rust inline) v6",
          "status": "COMPLETE",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00",
          "total_score": 0.603,
          "vina_score": -8.1106
        },
        "step_6_billing": {
          "internal_cost_usd": "0.23",
          "retail_price_usd": "650.00",
          "source": "Governed Billing Ledger",
          "status": "COMPLETE",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00"
        },
        "step_8_npead": {
          "chemistry_score": 0.905,
          "grade_logged": "A+",
          "is_membrane": false,
          "outcome_fed_to_maml": true,
          "pose_variance": 0.0,
          "source": "NPEAD Learning System",
          "status": "LOGGED",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00",
          "vina_logged": -8.1106
        },
        "step_9_intelligence": {
          "brain_bus_consulted": true,
          "cross_target_patterns": true,
          "failure_taxonomy_checked": true,
          "learned_knowledge_consulted": true,
          "smos_memories_queried": true,
          "source": "Cortex Intelligence Layer",
          "status": "COMPLETE",
          "timestamp": "2026-07-23T17:15:57.888390115+00:00"
        },
        "step_master_brain": {
          "action": "generate",
          "chosen_by": "",
          "consensus": {
            "arbitration": "",
            "llm_said": "",
            "rule_said": ""
          },
          "context": {
            "authority": 0.5,
            "failures": 0,
            "inhibitors": 8,
            "runs": 3
          },
          "directives": {
            "explore_ratio": 0.5,
            "focus": "balanced",
            "scaffold_hint": "",
            "weight_overrides": {}
          },
          "method": "rules_only",
          "rationale": "Standard generation \u2014 no signals require special handling",
          "risk": "",
          "timestamp": "2026-07-23T17:11:11.195806Z"
        }
      }
    },
    {
      "@type": "PerformanceMetrics",
      "@id": "#performance",
      "totalMs": 0,
      "nimMs": 0,
      "substrateMs": 0,
      "scorer": "smina_gpu"
    },
    {
      "@type": "Disclaimer",
      "@id": "#disclaimer",
      "text": "COMPUTATIONAL HYPOTHESIS \u2014 REQUIRES EXPERT VALIDATION BEFORE EXPERIMENTAL COMMITMENT"
    }
  ]
}