{
  "annotation_id": "f5a67120-f2e2-4943-bf74-e20f4ec25925",
  "date_created": "2026-03-02T18:01:31.934000Z",
  "date_modified": "2026-03-02T18:01:31.934000Z",
  "file_hash": "94c2ddcb997f8d0d1aa88f8a80d9fd74a823b3cd2ca046b158cc5f197f253b0b",
  "private": false,
  "record": {
    "abstract": "We present a base-pairing model of oligonuleotide duplex formation and show\nin detail its equivalence to the Nearest-Neighbour dimer methods from fits to\nfree energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids\ncontaining only Watson Crick pairs. In this approach the connection between\nrank-deficient polymer and rank-determinant oligonucleotide parameter, sets for\nDNA duplexes is transparent. The method is generalised to include RNA/DNA\nhybrids where the rank-deficient model with 11 dimer parameters in fact\nprovides marginally improved predictions relative to the standard method with\n16 independent dimer parameters ($\\Delta G$ mean errors of 4.5 and 5.4 %\nrespectively).",
    "arxiv_id": "q-bio/0507041",
    "authors": [
      "J. D. Bashford",
      "P. D. Jarvis"
    ],
    "categories": [
      "q-bio.BM"
    ],
    "doi": "10.1002/bip.20282",
    "journal_ref": "Biopolymers 78: 287-297, 2005",
    "title": "A base pairing model of duplex formation I: Watson-Crick pairing   geometries",
    "url": "https://arxiv.org/abs/q-bio/0507041"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "01674d9b-0084-4987-8f3b-96793c0f5cd0",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}