{
  "annotation_id": "92c90720-cace-4d84-b01f-2355ab59b1e2",
  "date_created": "2026-03-02T18:01:31.872000Z",
  "date_modified": "2026-03-02T18:01:31.872000Z",
  "file_hash": "9f739c4db167f8dbc519f2ea97ffb681beeb09e544eb8c67947911d48bf63703",
  "private": false,
  "record": {
    "abstract": "Here we study the effects of many-body interactions on rate and mechanism in\nprotein folding, using the results of molecular dynamics simulations on\nnumerous coarse-grained C-alpha-model single-domain proteins. After adding\nthree-body interactions explicitly as a perturbation to a Go-like Hamiltonian\nwith native pair-wise interactions only, we have found 1) a significantly\nincreased correlation with experimental phi-values and folding rates, 2) a\nstronger correlation of folding rate with contact order, matching the\nexperimental range in rates when the fraction of three-body energy in the\nnative state is ~ 20%, and 3) a considerably larger amount of 3-body energy\npresent in Chymotripsin inhibitor than other proteins studied.",
    "arxiv_id": "q-bio/0407019",
    "authors": [
      "M. R. Ejtehadi",
      "S. P. Avall",
      "S. S. Plotkin"
    ],
    "categories": [
      "q-bio.QM",
      "cond-mat.soft",
      "physics.bio-ph",
      "q-bio.BM"
    ],
    "doi": "10.1073/pnas.0403486101",
    "title": "Three-body Interactions Improve the Prediction of Rate and Mechanism in   Protein Folding Models",
    "url": "https://arxiv.org/abs/q-bio/0407019"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "409c7750-ebb2-4176-a966-5f2ad3926e50",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}