AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

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.