{
  "annotation_id": "6cb7e38b-f261-4d03-abe8-49c6191210ac",
  "date_created": "2026-03-02T18:01:31.873000Z",
  "date_modified": "2026-03-02T18:01:31.873000Z",
  "file_hash": "edc6f0e914f1beba5d8881e0c7e56e3f44af277272a94a17ff27d2323488d376",
  "private": false,
  "record": {
    "abstract": "Proteins are minimally frustrated polymers. However, for realistic protein\nmodels non-native interactions must be taken into account. In this paper we\nanalyze the effect of non-native interactions on the folding rate and on the\nfolding free energy barrier. We present an analytic theory to account for the\nmodification on the free energy landscape upon introduction of non-native\ncontacts, added as a perturbation to the strong native interactions driving\nfolding. Our theory predicts a rate-enhancement regime at fixed temperature,\nunder the introduction of weak, non-native interactions. We have thoroughly\ntested this theoretical prediction with simulations of a coarse-grained protein\nmodel, by employing an off-lattice $C_\\alpha$ model of the src-SH3 domain. The\nstrong agreement between results from simulations and theory confirm the non\ntrivial result that a relatively small amount of non-native interaction energy\ncan actually assist the folding to the native structure.",
    "arxiv_id": "q-bio/0407023",
    "authors": [
      "C. Clementi",
      "S. S. Plotkin"
    ],
    "categories": [
      "q-bio.BM"
    ],
    "journal_ref": "Protein Science 2004 13: 1750-1766",
    "title": "The effects of non-native interactions on protein folding rates: Theory   and simulation",
    "url": "https://arxiv.org/abs/q-bio/0407023"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "36710dc8-ec95-4da0-88e9-3a560dd237d6",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}