{
  "annotation_id": "5b0f3717-a3f6-4c45-85c6-79e34c8cdabd",
  "date_created": "2026-03-02T18:00:53.725000Z",
  "date_modified": "2026-03-02T18:00:53.725000Z",
  "file_hash": "e6426ce287dfea15ef80be27287769c9b695faaf655ef1e4af86e8d66ab889a5",
  "private": false,
  "record": {
    "abstract": "We study the conformational equilibria of two peptides using a novel\nstatistical mechanics approach designed for calculating free energy differences\nbetween highly dis-similar conformational states. Our results elucidate the\ncontrasting roles of entropy in implicitly solvated leucine dipeptide and\ndecaglycine. The method extends earlier work by Voter, and overcomes the\nnotorious \"overlap\" problem in free energy computations by constructing a\nmathematically equivalent calculation with high conformational similarity. The\napproach requires only equilibrium simulations of the two states of interest,\nwithout the need for sampling transition states. We discuss extensions of the\napproach to binding affinity estimation and explicitly solvated systems, as\nwell as possible optimizations.",
    "arxiv_id": "physics/0412116",
    "authors": [
      "F. Marty Ytreberg",
      "Daniel M. Zuckerman"
    ],
    "categories": [
      "physics.bio-ph"
    ],
    "title": "Peptide Conformational Equilibria Computed via a Single-Stage Shifting   Protocol",
    "url": "https://arxiv.org/abs/physics/0412116"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "b33ef37e-d390-407c-b863-3735ba3f3c21",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}