Molecular dynamics (MD) is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to MD, by replacing the integration of molecular systems over time with the training of generative neural networks. This neural network approach to MD enables convergence to thermodynamic equilibrium faster than traditional MD; however, critical gaps in the theory and computational feasibility of Boltzmann generators significantly reduce their usability. Here, we develop a mathematical foundation to overcome these barriers; we demonstrate that the Boltzmann generator approach is sufficiently rapid to replace traditional MD for complex macromolecules, such as proteins in specific applications, and we provide a comprehensive toolkit for the exploration of molecular energy landscapes with neural networks.

Traditional drug discovery pipelines can require multiple years and billions of dollars of investment. Deep generative and discriminative models are widely adopted to assist in drug development. Classical machines cannot efficiently reproduce the atypical patterns of quantum computers, which may improve the quality of learned tasks. We propose a suite of quantum machine learning techniques: incorporating generative adversarial networks (GAN), convolutional neural networks (CNN) and variational auto-encoders (VAE) to generate small drug molecules, classify binding pockets in proteins, and generate large drug molecules, respectively.