RealQM Reduced Model Database

Per-protein reduced-model JSON records generated by RealQM. Each entry is the output of one converged real-space multiphase computation, post-processed into a small record (~1 KB per protein) suitable as input to cell-scale Brownian-dynamics simulators. Use these JSONs to drive population dynamics of single or multiple species; see the main Gallery for working consumer demos.

1 entry, contributions welcome. See the directory on GitHub for the schema and contribution guide.

Available reduced models

PDB ID Species Sequence Residues Net q (e) Status Download
1UAO chignolin (β-hairpin) GYDPETGTWG 10 −2 partial sequence-derived; modes & surface TODO 1UAO.json

Planned entries (queue)

PDB ID Species Sequence length Why interesting
1L2Y Trp-cage 20 Smallest fast-folding mini-protein; well-characterised dynamics
1VII villin headpiece HP35 35 3-helix bundle; classic folding benchmark
1UBQ ubiquitin 76 Most-studied small folded domain
2OOB BPTI 58 Strong protease inhibitor, well-defined binding
4OO8 WW domain 34 All-β, complementary to villin

Schema

Each entry has the following structure (from 1UAO.json):

{
  "species": "chignolin",
  "pdb_id": "1UAO",
  "sequence": "GYDPETGTWG",
  "n_residues": 10,
  "n_atoms_heavy": 75,
  "energy_Ha": null,                          // converged RealQM total E
  "net_charge_e": -2,                         // sequence-derived (Asp/Glu/Lys/Arg)
  "mass_Da": 1100,
  "end_to_end_au": 18.0,
  "end_to_end_AA": 9.5,
  "bounding_box_au": { "x": [...], "y": [...], "z": [...] },
  "hydrodynamic_radius_au": 9.0,
  "hydrophobicity_avg_kd": -1.34,             // Kyte-Doolittle average
  "residues": [
    { "chain": "A", "num": 1, "name": "GLY", "aa": "G",
      "hydrophobicity_kd": -0.4, "sidechain_charge": 0 },
    ...
  ],
  "modes": "TODO",                            // C-alpha Hessian (~6N runs)
  "surface_electrostatic": "TODO",            // marching-cubes on density
  "provenance": {
    "method": "RealQM via molecule.js",
    "structure_source": "PDB 1UAO (Honda et al., Structure 2004)",
    "extraction_tool": "protein_reduce.html",
    "structure_url": "https://files.rcsb.org/download/1UAO.pdb"
  }
}

How to add an entry

  1. Open protein_reduce.html.
  2. Enter the PDB ID and click Fetch & run.
  3. Wait for the energy readout to stabilise (typical: 20–60 s for proteins under 30 residues).
  4. Click Extract now, inspect the JSON preview, then click Download JSON.
  5. Submit the file to the reduced_models/ directory via pull request, and add a row in the table above.