{
  "schema": "sma-public-research-dataset-v2",
  "title": "PERP designs: structures and membrane simulations",
  "date": "2026-09-12",
  "scope": {
    "target": "human PERP",
    "accession": "Q96FX8",
    "residues": "1–193",
    "candidates": 5,
    "original_pdb_files": 5,
    "oriented_pdb_files": 6,
    "membrane_final_pdb_files": 5,
    "membrane_metrics_files": 5,
    "complete_membrane_duration_ps": 520,
    "H2b_9_s2_recorded_checkpoint_ps": 510
  },
  "findings": [
    "The five candidates are H1a_38_s7, H1c_25_s4, H1c_25_s5, H2b_9_s2 and H2c_11_s1. Each uses human PERP, UniProt Q96FX8, residues 1–193. Exact binder and target sequences are available as structured identities and FASTA.",
    "The coordinate dataset contains five original pre-orientation structures and six oriented baseline structures, including PERP alone. Four binder complexes and the PERP-only comparison have complete 520 ps POPC coordinate/metrics pairs. Final PDBs retain the POPC, water and ion context.",
    "For H2b_9_s2, the available record documents a 510 ps checkpoint. No final 520 ps coordinate or complete metrics file is included. The distinction is preserved in the table and simulation summary.",
    "Separate aqueous-source simulations have 1,500 saved observations over 29.98 ns. Their full trajectories are not part of this dataset. The simulation summary preserves the recorded observation interval and duration without implying that these trajectories can be reproduced from the files provided here."
  ],
  "limitations": [
    "The POPC files are short computational coordinate and metric observations. They establish neither experimental binding, affinity, membrane convergence, accessibility, function nor an SMA-related effect.",
    "PERP alone is a structural comparison, not an experimentally established nonbinding control.",
    "The bundle is not a full molecular-dynamics reproduction. Full trajectories, checkpoints and complete simulation-system states are not included."
  ],
  "artifacts": [
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      "url": "artifacts/popc_qualification/h1a/final.pdb",
      "bytes": 8518731,
      "duration_ps": 520,
      "candidate_id": "H1a_38_s7",
      "format": "PDB structure"
    },
    {
      "url": "artifacts/popc_qualification/h1a/metrics.csv",
      "bytes": 52879,
      "duration_ps": 520,
      "candidate_id": "H1a_38_s7",
      "format": "Simulation metrics"
    },
    {
      "url": "artifacts/popc_qualification/h1c25s4/final.pdb",
      "bytes": 8714950,
      "duration_ps": 520,
      "candidate_id": "H1c_25_s4",
      "format": "PDB structure"
    },
    {
      "url": "artifacts/popc_qualification/h1c25s4/metrics.csv",
      "bytes": 52566,
      "duration_ps": 520,
      "candidate_id": "H1c_25_s4",
      "format": "Simulation metrics"
    },
    {
      "url": "artifacts/popc_qualification/h1c25s5/final.pdb",
      "bytes": 8732365,
      "duration_ps": 520,
      "candidate_id": "H1c_25_s5",
      "format": "PDB structure"
    },
    {
      "url": "artifacts/popc_qualification/h1c25s5/metrics.csv",
      "bytes": 52604,
      "duration_ps": 520,
      "candidate_id": "H1c_25_s5",
      "format": "Simulation metrics"
    },
    {
      "url": "artifacts/popc_qualification/h2c11s1/final.pdb",
      "bytes": 18881553,
      "duration_ps": 520,
      "candidate_id": "H2c_11_s1",
      "format": "PDB structure"
    },
    {
      "url": "artifacts/popc_qualification/h2c11s1/metrics.csv",
      "bytes": 52561,
      "duration_ps": 520,
      "candidate_id": "H2c_11_s1",
      "format": "Simulation metrics"
    },
    {
      "url": "artifacts/popc_qualification/perp/final.pdb",
      "bytes": 7239228,
      "duration_ps": 520,
      "candidate_id": "PERP_alone",
      "format": "PDB structure"
    },
    {
      "url": "artifacts/popc_qualification/perp/metrics.csv",
      "bytes": 47410,
      "duration_ps": 520,
      "candidate_id": "PERP_alone",
      "format": "Simulation metrics"
    },
    {
      "url": "identity.json",
      "bytes": 1877,
      "format": "Structured data"
    },
    {
      "url": "public_run_summary.json",
      "bytes": 4249,
      "format": "Structured data"
    },
    {
      "url": "sequences.fasta",
      "bytes": 791,
      "format": "Protein sequences"
    },
    {
      "url": "structures/oriented_baseline/PERP_alone.pdb",
      "bytes": 121996,
      "candidate_id": "PERP_alone",
      "format": "PDB structure"
    },
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      "url": "structures/oriented_baseline/design_H1a_38_s7.pdb",
      "bytes": 174327,
      "candidate_id": "H1a_38_s7",
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      "format": "PDB structure"
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      "url": "structures/oriented_baseline/design_H1c_25_s5.pdb",
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      "format": "PDB structure"
    },
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      "format": "PDB structure"
    },
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      "format": "PDB structure"
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}