{
  "abstract": "Systematic evolution of ligands by exponential enrichment (SELEX)-based aptamer discovery can be constrained by target availability, selection biases, and optimization requirements. We introduce Xelari, a modular pipeline for de novo DNA and RNA aptamer design from protein structures without target-specific SELEX data or retraining. Xelari combines algorithmic modules with surrogate models trained on physical or structural references. InNA reproduced nucleotide-amino-acid interaction energies with RMSE of 0.19 kcal/mol across 483,735 reference pairs. AliNA achieved a mean F1 of 0.757 on 339 PDB-derived RNA evaluation sequences. Edgar correlated with experimental folding energies but did not reproduce their absolute scale, supporting its use as a ranking heuristic. Under the reported calibration, ValentiNA showed MAE of 0.931 kcal/mol and Spearman ρ of 0.795 across 32 retrospective records associated with 27 structural templates; this analysis does not establish family-independent validation. Prospectively, three DNA aptamers designed against Treponema pallidum protein structures showed cell-associated binding in a treponeme assay (apparent K D , 0.91–2.57 μM). A fourth DNA aptamer served as a capture reagent in a serum-based hybrid aptamer-antibody assay for Tau441. These applications support feasibility without establishing intended-target engagement in the cellular assay or a general success rate, positioning structure-based design as a complement to experimental selection.",
  "abstract_shown": true,
  "affiliations": [
    "Xelari Inc., 8 The Green B, Dover, DE 19901, USA; Corresponding author: Vladislava A. Dolgusheva, Xelari Inc., 8 The Green B, Dover, DE 19901, USA.",
    "Xelari Inc., 8 The Green B, Dover, DE 19901, USA",
    "Mad Devs LLC, 103 Ibraimova str., Bishkek 720011, Kyrgyzstan"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 17,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Vladislava A. Dolgusheva"
    },
    {
      "affs": [
        1
      ],
      "name": "Iosif V. Leibin"
    },
    {
      "affs": [
        1
      ],
      "name": "Natalia O. Kudryashova"
    },
    {
      "affs": [
        1
      ],
      "name": "Artem R. Mukanov"
    },
    {
      "affs": [
        1
      ],
      "name": "Ivan I. Kuznetsov"
    },
    {
      "affs": [
        1
      ],
      "name": "Artem L. Manasyan"
    },
    {
      "affs": [
        1
      ],
      "name": "Gleb A. Pavlyuk"
    },
    {
      "affs": [
        1
      ],
      "name": "Ivan V. Mishkorez"
    },
    {
      "affs": [
        1
      ],
      "name": "Anna M. Keremet"
    },
    {
      "affs": [
        1
      ],
      "name": "Pavel R. Podlesnyi"
    },
    {
      "affs": [
        1
      ],
      "name": "Alexey N. Kalinkin"
    },
    {
      "affs": [
        2
      ],
      "name": "Kirill S. Avdeev"
    },
    {
      "affs": [
        2
      ],
      "name": "Maxim D. Kuznetsov"
    },
    {
      "affs": [
        1
      ],
      "name": "Nikita O. Parfenov"
    },
    {
      "affs": [
        1
      ],
      "name": "Stanislav M. Gromov"
    },
    {
      "affs": [
        1
      ],
      "name": "Dmitry Ufaev"
    },
    {
      "affs": [
        1
      ],
      "name": "Shamsudin S. Nasaev"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fxmc10gbrg5h1.bib",
  "cited_by": 0,
  "doi": "10.1016/j.omtn.2026.103133",
  "fulltext_url": "http://www.sciencedirect.com/science/article/pii/S2162253126003045",
  "id": "fxmc10gbrg5h1",
  "issns": [
    "2162-2531"
  ],
  "landing_url": "https://doi.org/10.1016/j.omtn.2026.103133",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Original Article"
    ],
    [
      "lcc",
      "RM1-950"
    ],
    [
      "openalex",
      "1312|Advanced biosensing and bioanalysis techniques"
    ]
  ],
  "openalex": "W7220900796",
  "pdf_url": "https://europepmc.org/articles/PMC13718419?pdf=render",
  "pmcid": null,
  "pmid": "42960155",
  "published": "2026-10-07",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/fxmc10gbrg5h1.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:44:35Z",
      "native_id": "a8609b8db5b649db89aa046bae3feae1",
      "source": "doaj",
      "url": "https://doi.org/10.1016/j.omtn.2026.103133"
    },
    {
      "first_seen": "2026-11-01T00:20:52Z",
      "native_id": "MED:42960155",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42960155"
    },
    {
      "first_seen": "2026-11-02T12:22:27Z",
      "native_id": "PMC13718419",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.omtn.2026.103133"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Advanced biosensing and bioanalysis techniques",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Aptamers without SELEX:",
  "title_text": "Aptamers without SELEX:",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:27Z",
  "url": "https://research.draconitic.com/paper/fxmc10gbrg5h1",
  "venue": "Molecular Therapy: Nucleic Acids",
  "versions": []
}