{
  "annotation_id": "644680e1-a634-4458-a87a-fc9f7c1695fe",
  "date_created": "2026-03-02T18:01:31.155000Z",
  "date_modified": "2026-03-02T18:01:31.155000Z",
  "file_hash": "bb5fad1ea7ffaac0c6aca7596702959c99d7ba9a05c1ed092ef6c262a3c035a0",
  "private": false,
  "record": {
    "abstract": "We present a verified computational model of the SH3 domain transition state\n(TS) ensemble. This model was built for three separate SH3 domains using\nexperimental s in all-atom protein folding simulations. While averaging over\nall conformations incorrectly considers non-TS conformations as transition\nstates, quantifying structures as pre-TS, TS, and post-TS by measurement of\ntheir transmission coefficient (pfold, or probability to fold) allows for\nrigorous conclusions regarding the structure of the folding nucleus and a full\nmechanistic analysis of the folding process. Through analysis of the TS, we\nobserve a highly polarized nucleus in which many residues are solvent-exposed.\nMechanistic analysis suggests the hydrophobic core forms largely after an early\nnucleation step. SH3 presents an ideal system for studying the\nnucleation-condensation mechanism and highlights the synergistic relationship\nbetween experiment and simulation in the study of protein folding.",
    "arxiv_id": "q-bio/0503027",
    "authors": [
      "Isaac A. Hubner",
      "Katherine A. Edmonds",
      "Eugene I. Shakhnovich"
    ],
    "categories": [
      "q-bio.BM",
      "q-bio.OT"
    ],
    "title": "Nucleation and the transition state of the SH3 domain",
    "url": "https://arxiv.org/abs/q-bio/0503027"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "04383f69-58bb-454c-8137-03c76e913eb0",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}