QO-BRA: A Quantum Operator-Based Autoencoder for De Novo Molecular Design

We introduce a variational quantum autoencoder tailored for de novo molecular design, named QO-BRA (Quantum Operator-Based Real Amplitude autoencoder). QO-BRA leverages quantum circuits for real-amplitude encoding and the SWAP test to estimate reconstruction and latent-space regularization errors during back-propagation. Adjoint encoder and decoder operators enable unitary transformations and a generative process that ensures accurate reconstruction, as well as the novelty, uniqueness, and validity of the generated samples. We showcase the capabilities of QO-BRA as applied to the de novo design of Ca²⁺-, Mg²⁺-, and Zn²⁺-binding metalloproteins after training the generative model with a modest data set.