AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

2026 · doi:10.64898/2026.01.06.698056
preprint OA: closed
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The paper presents AptaBLE, a deep learning framework designed to predict aptamer–protein binding and to reduce the time and experimental bias associated with aptamer discovery. Using two de novo generation methods, the authors generate novel aptamers with desired specificity profiles and report Kd values as low as 31 nM to date. The key limitation stated is that, per the footnote, the revision work adds in vitro experimental data collected after the initial revision, implying that the current results include updates beyond the originally submitted materials. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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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 K d ’s as low as 31 nM to-date. AptaBLE represents a significant advance towards therapeutic and diagnostic aptamer development.
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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 Kd’s as low as 31 nM to-date. AptaBLE represents a significant advance towards therapeutic and diagnostic aptamer development. Competing Interest Statement A patent application related to this work has been filed by Atom Bioworks (No. 19/398,384), listing S.P and S.Y as the inventors. P.C, X.W, and S.Y. are co-founders of Atom Bioworks. S.P is an employee at Atom Bioworks. K.F. is a Science Advisor at Atom Bioworks. F.Z.P, D.G, and A.D. declare no competing interests. Footnotes Revision includes in vitro experimental data which has been collected since the first revision was submitted to bioRxiv.

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last seen: 2026-05-20T01:45:00.602351+00:00