{
  "record_type": "Published-method transcription; not an independent rerun",
  "source_page": "https://ugurcemyildiz.me/research/structure-based-drug-design/",
  "receptor": {
    "pdb_id": "3ODU",
    "resolution_angstrom": 2.5
  },
  "docking": {
    "software": "AutoDock Vina",
    "version": "1.1.2",
    "exhaustiveness": 32,
    "box_size_angstrom": [
      52,
      52,
      52
    ],
    "centre_angstrom": [
      19.78,
      -6.85,
      68.11
    ]
  },
  "preparation": {
    "receptor": "Waters, co-crystallised antagonist and non-protein heteroatoms removed; polar hydrogens and Kollman charges added with AutoDock Tools.",
    "ligands": "Designed with MolSoft ICM-Chemist; 3D coordinates and minimisation with NCI SMILES Translator; Gasteiger charges and rotatable bonds assigned with AutoDock Tools."
  },
  "predictions": [
    "SwissADME",
    "ProTox-II"
  ],
  "results_csv": "/research-data/docking-results.csv",
  "displayed_pose": {
    "path": "/structures/cxcr4-fluoro-deoxy-amentoflavone.pdb",
    "description": "Prepared receptor and Fluoro-Deoxy-Amentoflavone Vina pose 1; hydrogens removed for web display.",
    "sha256": "014122a2a18b98647e13f6232e2e8063937542aaa55278e9760b9cc1dbb6b0c9",
    "labelled_residues": [
      {
        "number": 43,
        "names": [
          "ASN"
        ]
      },
      {
        "number": 55,
        "names": [
          "TYR"
        ]
      },
      {
        "number": 104,
        "names": [
          "TRP"
        ]
      },
      {
        "number": 196,
        "names": [
          "CYS"
        ]
      },
      {
        "number": 429,
        "names": [
          "TYR"
        ]
      }
    ]
  },
  "unavailable": [
    "analysis_date",
    "random_seed",
    "full_ligand_inputs",
    "original_vina_configuration_file",
    "run_logs",
    "independent_replication"
  ],
  "interpretation": "Docking and ADME/toxicity predictions do not establish biological activity or clinical safety."
}