{
  "schema": "sma-public-research-dataset-v2",
  "title": "Binder10246: KEAP1 construct comparison",
  "date": "2026-09-12",
  "scope": {
    "binder": "Binder10246",
    "binder_length_aa": 118,
    "target": "KEAP1",
    "constructs": [
      {
        "residues": "315–624",
        "models": 15
      },
      {
        "residues": "325–609",
        "models": 15
      }
    ],
    "seeds": [
      7,
      42,
      101
    ],
    "samples_per_seed": 5,
    "coordinate_files": 30,
    "confidence_files": 30,
    "compact_inputs": 2
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  "findings": [
    "The two KEAP1 constructs each have 15 models: seeds 7, 42 and 101, with five samples per seed. The same exact 118-residue binder sequence is used in both arms. All 30 original coordinate files and 30 matching confidence summaries are available below.",
    "Across the 15 numerically matched pairs, the median extended-minus-short iPTM difference is −0.01. Common-core residue-pair contact counts change by medians of +5 at 4 Å and +14 at 5 Å. Contacts are target–binder residue pairs with at least one heavy-atom separation within the stated distance, not atom-pair totals.",
    "After fitting the shared target core, median binder-placement RMSD is 9.959 Å. Seed medians are 3.701 Å for seed 7, 18.027 Å for seed 42 and 6.855 Å for seed 101. Median common-target core-fit RMSD is 0.212 Å and binder self-fit RMSD is 0.420 Å. This combination indicates heterogeneous relative placement despite a much smaller within-chain structural difference.",
    "Neither the added N-terminal segment nor the added C-terminal segment directly contacts the binder in any of the 15 extended-construct models at 4 or 5 Å. Absence of these contacts does not make the two modeling contexts equivalent, because the additional target sequence changes the represented molecular context."
  ],
  "limitations": [
    "The 30 outputs are dependent computational realizations, not 30 independent experiments. Numerical seed/sample pairing does not isolate every source of stochastic variation.",
    "Contacts, PAE, iPTM and geometry establish neither binding, affinity, NRF2 competition, intracellular activity, NRF2 function nor an SMA-related effect.",
    "Compact inputs preserve exact sequence, construct and seed identities, but omit enriched inference features, complete confidence matrices, multiple-sequence alignments and templates. They cannot reproduce the full inference by themselves.",
    "The older Binder10246 model series is a separate comparison and is not included in these counts."
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        "42": 18.027037139814734,
        "101": 6.855356726608297
      },
      "common_target_core_fit_rmsd_median_A": 0.21161552371650677,
      "binder_self_fit_rmsd_median_A": 0.4196265728557142
    },
    "contact_metric_definition": "common-core contact counts are target-binder residue-pair counts with at least one heavy-atom distance at or below the stated 4 A or 5 A cutoff; they are not atom-pair totals"
  }
}