ArticleJournal of chemical information and modeling2026
APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.
Article in Journal of chemical information and modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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3 authors.
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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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