Workshop: Machine Learning in Structural Biology

MOLUCINATE: A Generative Model for Molecules in 3D Space

Michael Brocidiacono · David Koes


Recent advances in machine learning have enabled generative models for both optimization and de novo generation of drug candidates with desired properties. Previous generative models have focused on producing SMILES strings or 2D molecular graphs, while attempts at producing molecules in 3D have focused on reinforcement learning (RL), distance matrices, and pure atom density grids. Here we present MOLUCINATE (MOLecUlar ConvolutIoNal generATive modEl), a novel architecture that simultaneously generates topological and 3D atom position information. We demonstrate the utility of this method by using it to optimize molecules for desired radius of gyration. In the future, this model can be used for more useful optimization such as binding affinity against a protein target.

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