{
  "annotation_id": "8e75e261-3426-4e51-999e-7b9891d27827",
  "date_created": "2026-03-02T18:01:35.376000Z",
  "date_modified": "2026-03-02T18:01:35.376000Z",
  "file_hash": "39dcfb0ab151aff11a68370aac674e3006bc380c3dc06d8a67927aa533b9dc39",
  "private": false,
  "record": {
    "abstract": "Natural proteins fold to a unique, thermodynamically dominant state. Modeling\nof the folding process and prediction of the native fold of proteins are two\nmajor unsolved problems in biophysics. Here, we show successful all-atom ab\ninitio folding of a representative diverse set of proteins, using a minimalist\ntransferable energy model that consists of two-body atom-atom interactions,\nhydrogen-bonding, and a local sequence energy term that models\nsequence-specific chain stiffness. Starting from a random coil, the native-like\nstructure was observed during replica exchange Monte Carlo (REMC) simulation\nfor most proteins regardless of their structural classes; the lowest energy\nstructure was close to native- in the range of 2-6 A root-mean-square deviation\n(RMSD). Our results demonstrate that the successful all-atom folding of a\nprotein chain to its native state is governed by only a few crucial energetic\nterms.",
    "arxiv_id": "q-bio/0611086",
    "authors": [
      "Jae Shick Yang",
      "William W. Chen",
      "Jeffrey Skolnick",
      "Eugene I. Shakhnovich"
    ],
    "categories": [
      "q-bio.BM"
    ],
    "title": "All-atom ab initio folding of a diverse set of proteins",
    "url": "https://arxiv.org/abs/q-bio/0611086"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "83cac6d9-00ba-4edb-b1ff-ba34abf58cfc",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}