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bioRxiv · 10.64898/2026.01.06.698056

AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

Patel, S.·Peng, F. Z.·Fraser, K.·Dwivedy, A.·Gandavadi, D.·Wang, X.·Chatterjee, P.·Yao, S.
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Abstract

Aptamers are single-stranded oligonucleotides that bind molecular targets with high affinity and specificity. However, their discovery remains time-consuming, expensive, and susceptible to experimental biases. Here we present AptaBLE, a deep learning framework for predicting aptamer-protein binding. Additionally, we demonstrate two de novo generation methods that produce novel aptamers with desired specificity profiles and Kds as low as 31 nM to-date. AptaBLE represents a significant advance towards therapeutic and diagnostic aptamer development.

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Patel, S., Peng, F. Z., Fraser, K., Dwivedy, A., Gandavadi, D., Wang, X., Chatterjee, P., Yao, S.. 2026-01-07. AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis. https://doi.org/10.64898/2026.01.06.698056

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