{
  "release_slug": "binder-reference-context-20260913-v1",
  "title": "Reference-context analysis for Binder10246 and two NCALD designs",
  "a05": {
    "binder": {
      "name": "Binder10246",
      "length": 118,
      "sequence": "EVQLVESGGGLVQAGGSLRLSCAASGFTFSSYYMGWYRQAPGKERELVARISSDGSTTYYADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARYDPITGWADYWGQGTQVTVS"
    },
    "target": {
      "organism": "Homo sapiens",
      "accession": "Q14145",
      "constructs": [
        "315-624",
        "325-609"
      ]
    },
    "reference": {
      "structure": "PDB 5WFV",
      "receptor_chain": {
        "label_asym_id": "A",
        "auth_asym_id": "A"
      },
      "peptide_chain": {
        "label_asym_id": "C",
        "auth_asym_id": "P"
      },
      "peptide": "NRF2 LDEETGEFL",
      "peptide_length": 9,
      "contact_mask_denominators": {
        "4A": 16,
        "5A": 22
      }
    },
    "method": {
      "fit_positions": "canonical KEAP1 positions 326-609 with resolved C-alpha atoms, excluding positions 540 and 542",
      "fit_position_count": 282,
      "contact_mask_intersection": "Shared canonical KEAP1 positions in the reference and model contact sets at the stated cutoff.",
      "spatial_overlap": "Heavy-atom distances between the transformed Binder10246 and the fixed 5WFV NRF2 peptide.",
      "sequence_deviation_positions_in_reference_or_model_contact_masks": []
    },
    "canonical_sequence_differences_in_5wfv": [
      {
        "position": 319,
        "canonical": "C",
        "observed": "S",
        "explicitly_annotated_as_mutation": false
      },
      {
        "position": 540,
        "canonical": "E",
        "observed": "A",
        "explicitly_annotated_as_mutation": true
      },
      {
        "position": 542,
        "canonical": "E",
        "observed": "A",
        "explicitly_annotated_as_mutation": true
      },
      {
        "position": 613,
        "canonical": "C",
        "observed": "S",
        "explicitly_annotated_as_mutation": false
      },
      {
        "position": 622,
        "canonical": "C",
        "observed": "S",
        "explicitly_annotated_as_mutation": false
      },
      {
        "position": 624,
        "canonical": "C",
        "observed": "S",
        "explicitly_annotated_as_mutation": false
      }
    ],
    "model_count": 30,
    "all_models_etge_residues_within_4A": "9/9",
    "groups": [
      {
        "arm": "extended_315_624",
        "seed": "7",
        "n": "5",
        "fit_rmsd_median_A": "0.27864850375926153",
        "fit_rmsd_min_A": "0.2618926980849076",
        "fit_rmsd_max_A": "0.3207139478672668",
        "mask4_intersection_median": "16",
        "mask4_intersection_min": "16",
        "mask4_intersection_max": "16",
        "mask5_intersection_median": "20",
        "mask5_intersection_min": "20",
        "mask5_intersection_max": "21",
        "spatial4_binder_median": "20",
        "spatial4_binder_min": "19",
        "spatial4_binder_max": "22",
        "spatial5_binder_median": "26",
        "spatial5_binder_min": "24",
        "spatial5_binder_max": "28",
        "spatial4_peptide_median": "9",
        "spatial5_peptide_median": "9"
      },
      {
        "arm": "extended_315_624",
        "seed": "42",
        "n": "5",
        "fit_rmsd_median_A": "0.28016723458586523",
        "fit_rmsd_min_A": "0.26856068596507987",
        "fit_rmsd_max_A": "0.2995259809890706",
        "mask4_intersection_median": "16",
        "mask4_intersection_min": "15",
        "mask4_intersection_max": "16",
        "mask5_intersection_median": "19",
        "mask5_intersection_min": "19",
        "mask5_intersection_max": "20",
        "spatial4_binder_median": "19",
        "spatial4_binder_min": "18",
        "spatial4_binder_max": "24",
        "spatial5_binder_median": "24",
        "spatial5_binder_min": "23",
        "spatial5_binder_max": "29",
        "spatial4_peptide_median": "9",
        "spatial5_peptide_median": "9"
      },
      {
        "arm": "extended_315_624",
        "seed": "101",
        "n": "5",
        "fit_rmsd_median_A": "0.2913261672040498",
        "fit_rmsd_min_A": "0.2646855715511771",
        "fit_rmsd_max_A": "0.2950711274908992",
        "mask4_intersection_median": "15",
        "mask4_intersection_min": "14",
        "mask4_intersection_max": "16",
        "mask5_intersection_median": "19",
        "mask5_intersection_min": "18",
        "mask5_intersection_max": "19",
        "spatial4_binder_median": "20",
        "spatial4_binder_min": "18",
        "spatial4_binder_max": "21",
        "spatial5_binder_median": "23",
        "spatial5_binder_min": "21",
        "spatial5_binder_max": "26",
        "spatial4_peptide_median": "9",
        "spatial5_peptide_median": "9"
      },
      {
        "arm": "short_325_609",
        "seed": "7",
        "n": "5",
        "fit_rmsd_median_A": "0.3672888238669305",
        "fit_rmsd_min_A": "0.2997952645263765",
        "fit_rmsd_max_A": "0.4312593773808273",
        "mask4_intersection_median": "14",
        "mask4_intersection_min": "13",
        "mask4_intersection_max": "16",
        "mask5_intersection_median": "17",
        "mask5_intersection_min": "16",
        "mask5_intersection_max": "19",
        "spatial4_binder_median": "17",
        "spatial4_binder_min": "14",
        "spatial4_binder_max": "21",
        "spatial5_binder_median": "23",
        "spatial5_binder_min": "22",
        "spatial5_binder_max": "24",
        "spatial4_peptide_median": "9",
        "spatial5_peptide_median": "9"
      },
      {
        "arm": "short_325_609",
        "seed": "42",
        "n": "5",
        "fit_rmsd_median_A": "0.34441342241461287",
        "fit_rmsd_min_A": "0.3397314138238085",
        "fit_rmsd_max_A": "0.3573236733030426",
        "mask4_intersection_median": "10",
        "mask4_intersection_min": "10",
        "mask4_intersection_max": "12",
        "mask5_intersection_median": "15",
        "mask5_intersection_min": "14",
        "mask5_intersection_max": "16",
        "spatial4_binder_median": "14",
        "spatial4_binder_min": "13",
        "spatial4_binder_max": "15",
        "spatial5_binder_median": "16",
        "spatial5_binder_min": "15",
        "spatial5_binder_max": "17",
        "spatial4_peptide_median": "9",
        "spatial5_peptide_median": "9"
      },
      {
        "arm": "short_325_609",
        "seed": "101",
        "n": "5",
        "fit_rmsd_median_A": "0.2946504216143425",
        "fit_rmsd_min_A": "0.27739015111352955",
        "fit_rmsd_max_A": "0.34418563537250446",
        "mask4_intersection_median": "16",
        "mask4_intersection_min": "13",
        "mask4_intersection_max": "16",
        "mask5_intersection_median": "19",
        "mask5_intersection_min": "18",
        "mask5_intersection_max": "20",
        "spatial4_binder_median": "18",
        "spatial4_binder_min": "14",
        "spatial4_binder_max": "22",
        "spatial5_binder_median": "24",
        "spatial5_binder_min": "17",
        "spatial5_binder_max": "25",
        "spatial4_peptide_median": "9",
        "spatial5_peptide_median": "9"
      }
    ],
    "interpretation_limit": "Geometric co-localization of separately determined poses; no evidence of binding, affinity, NRF2 displacement or cellular activation."
  },
  "a34": {
    "target_references": [
      {
        "organism": "Homo sapiens",
        "taxon_id": 9606,
        "accession": "P61601",
        "length": 193,
        "sequence_version": 2,
        "entry_version": 175
      },
      {
        "organism": "Mus musculus",
        "taxon_id": 10090,
        "accession": "Q91X97",
        "length": 193,
        "sequence_version": 4,
        "entry_version": 183
      }
    ],
    "reference_sequence_identity": "193/193",
    "terminal_residues": "Q192/F193",
    "target_sequence": "MGKQNSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKAEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQCDPSSAGQF",
    "designs": [
      {
        "name": "design_0154",
        "binder_length": 64,
        "binder_sequence": "AEEEREEEERRREEEEREREERAAKAREEFEALPEPIRRTFELIKEATEKDLQEVKELAEARKR"
      },
      {
        "name": "design_0026",
        "binder_length": 67,
        "binder_sequence": "SEEDKKLSEYLKRKFKVALDGLFGFFPEVKEEEEEEEEERRRREEEERRRREEREREEEERRRLEEL"
      }
    ],
    "source_backbone_masks": [
      {
        "design": "design_0026.pdb",
        "cutoff_A": 4,
        "unique_target_position_count": 4,
        "target_positions": "92;184;185;186"
      },
      {
        "design": "design_0026.pdb",
        "cutoff_A": 5,
        "unique_target_position_count": 9,
        "target_positions": "33;92;93;183;184;185;186;187;188"
      },
      {
        "design": "design_0026.pdb",
        "cutoff_A": 8,
        "unique_target_position_count": 25,
        "target_positions": "29;30;32;33;34;36;37;88;89;90;91;92;93;94;100;104;180;181;183;184;185;186;187;188;189"
      },
      {
        "design": "design_0154.pdb",
        "cutoff_A": 4,
        "unique_target_position_count": 0,
        "target_positions": ""
      },
      {
        "design": "design_0154.pdb",
        "cutoff_A": 5,
        "unique_target_position_count": 5,
        "target_positions": "54;92;93;174;175"
      },
      {
        "design": "design_0154.pdb",
        "cutoff_A": 8,
        "unique_target_position_count": 35,
        "target_positions": "26;29;30;31;32;33;34;36;37;50;51;53;54;55;56;57;58;89;91;92;93;94;95;96;97;173;174;175;176;177;178;180;181;184;186"
      }
    ],
    "terminal_support": [
      {
        "design": "design_0026.pdb",
        "cutoff_A": "4",
        "Q192_samples": "1",
        "F193_samples": "1",
        "Q192_or_F193_samples": "2",
        "sample_denominator": "15"
      },
      {
        "design": "design_0026.pdb",
        "cutoff_A": "5",
        "Q192_samples": "1",
        "F193_samples": "1",
        "Q192_or_F193_samples": "2",
        "sample_denominator": "15"
      },
      {
        "design": "design_0026.pdb",
        "cutoff_A": "8",
        "Q192_samples": "5",
        "F193_samples": "5",
        "Q192_or_F193_samples": "7",
        "sample_denominator": "15"
      },
      {
        "design": "design_0154.pdb",
        "cutoff_A": "4",
        "Q192_samples": "3",
        "F193_samples": "1",
        "Q192_or_F193_samples": "4",
        "sample_denominator": "15"
      },
      {
        "design": "design_0154.pdb",
        "cutoff_A": "5",
        "Q192_samples": "5",
        "F193_samples": "2",
        "Q192_or_F193_samples": "6",
        "sample_denominator": "15"
      },
      {
        "design": "design_0154.pdb",
        "cutoff_A": "8",
        "Q192_samples": "12",
        "F193_samples": "13",
        "Q192_or_F193_samples": "13",
        "sample_denominator": "15"
      }
    ],
    "interpretation_limit": "Reference-sequence identity and projected model contacts do not establish reagent identity, equal affinity, post-translational state, function or efficacy in mouse."
  },
  "downloads": {
    "a05_models": "https://sma-research.info/research-artifacts/a05-native10246-20260912-v1/",
    "a34_models": "https://sma-research.info/research-artifacts/a34-ncald-full193-20260912-v1/"
  }
}