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Peer-reviewedCC BYJournal of chemical information and modeling

APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.

  • Kabelo P Mokgopa1
  • Kevin A Lobb1,2
  • Tendamudzimu Tshiwawa1
  1. 1Department of Chemistry, Rhodes University, Makhanda6140, South Africa.
  2. 2Research Unit in Bioinformatics (RUBi), Rhodes University, Makhanda6140South Africa.
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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).

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Cite

BibTeXRIS
BibTeX
@article{mokgopa2026apdb,
  title = {{APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.}},
  author = {Kabelo P Mokgopa and Kevin A Lobb and Tendamudzimu Tshiwawa},
  journal = {Journal of chemical information and modeling},
  year = {2026},
  month = sep,
  doi = {10.1021/acs.jcim.6c02031},
  url = {https://europepmc.org/article/MED/42906068},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.
AU  - Kabelo P Mokgopa
AU  - Kevin A Lobb
AU  - Tendamudzimu Tshiwawa
PY  - 2026
DA  - 2026/09/01
JO  - Journal of chemical information and modeling
DO  - 10.1021/acs.jcim.6c02031
UR  - https://europepmc.org/article/MED/42906068
AB  - 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).
SN  - 1549-9596
SN  - 1549-960X
ER  -