{
  "abstract": "RNA aptamers are short, single-stranded oligonucleotides capable of folding into specific three-dimensional structures to bind diverse molecular targets with high affinity and specificity. In this study, we present a comprehensive computational analysis of a curated data set of over 150,000 RNA aptamers annotated with sequences, predicted secondary structures, molecular features, and minimum free energy (MFE) values. A total of 161 molecular descriptors were extracted, including pairing ratios, stem density, sequence complexity, and motif composition. Dimensionality reduction using Principal Component Analysis (PCA) and t-distributed Stochastic Neighbor Embedding (t-SNE) revealed distinct clustering patterns driven by MFE, GC/AU pairing composition, and secondary structure complexity. PCA indicated that aptamers with high AU content tend to occupy distinct structural space, while t-SNE highlighted concentrated regions of high GC pairing and stem density. A 3D surface plot of GC pairing, AU pairing, and MFE further demonstrated a nonlinear landscape, with folding stability changing in a bumpy, hill-like pattern as pairing ratios varied. These findings provide insights into how base-pairing composition influences aptamer folding stability and offer a framework for rational design. The resulting Aptamer Database (APDB) integrates these analyses into an interactive, scalable platform to support research in biosensing, therapeutics, and computational aptamer design (https://boron.ru.ac.za/database).",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, Rhodes University, Makhanda6140, South Africa.",
    "Research Unit in Bioinformatics (RUBi), Rhodes University, Makhanda6140South Africa."
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Kabelo P Mokgopa",
      "orcid": "0000-0001-8641-0892"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Kevin A Lobb",
      "orcid": "0000-0003-3023-0790"
    },
    {
      "affs": [
        0
      ],
      "name": "Tendamudzimu Tshiwawa"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/06xy0sa630r6r.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jcim.6c02031",
  "fulltext_url": "https://europepmc.org/articles/PMC13625953",
  "id": "06xy0sa630r6r",
  "issns": [
    "1549-9596",
    "1549-960X"
  ],
  "landing_url": "https://europepmc.org/article/MED/42906068",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|RNA and protein synthesis mechanisms"
    ]
  ],
  "openalex": "W7213461142",
  "pdf_url": "https://europepmc.org/articles/PMC13625953?pdf=render",
  "pmcid": "PMC13625953",
  "pmid": "42906068",
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/06xy0sa630r6r.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:57Z",
      "native_id": "MED:42906068",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42906068"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|RNA and protein synthesis mechanisms",
      "subfield": "molecular-biology"
    }
  ],
  "title": "APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.",
  "title_text": "APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:57Z",
  "url": "https://research.draconitic.com/paper/06xy0sa630r6r",
  "venue": "Journal of chemical information and modeling",
  "versions": []
}