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Workshop: Machine Learning in Structural Biology Workshop

Target-Aware Variational Auto-Encoders for Ligand Generation with Multi-Modal Protein Modeling

Khang Ngo · Truong Son Hy


Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline. However, contemporary methods require optimizing tailored networks for each protein, which is arduous and costly. To address this issue, we introduce TargetVAE, a target-aware variational auto-encoder that generates ligands with high binding affinities to arbitrary protein targets, guided by a novel prior network that learns from entire protein structures. We showcase the superiority of our approach by conducting extensive experiments and evaluations, including the assessment of generative model quality, ligand generation for unseen targets, docking score computation, and binding affinity prediction. Empirical results demonstrate the promising performance of our proposed approach. Our source code in PyTorch is publicly available at

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