Molecule Generation
In structure-based drug design (SBDD), a major challenge is generating high-affinity 3D ligand molecules that can effectively bind to specific protein targets, which requires accurately capturing complex protein-ligand interactions. Although existing diffusion models have demonstrated potential in molecular generation tasks, they often struggle with accurately capturing the complex interactions between proteins and ligands. To address this problem, we propose MSIDiff, a multi-stage interaction-aware diffusion model for protein-specific molecular generation.
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Expanding our knowledge of small molecules beyond what is known in nature or designed in wet laboratories promises to significantly advance drug discovery, biotechnology, and material science. Computing novel small molecules with specific structural and functional properties is non-trivial, primarily due to the size, dimensionality, and multi-modality of the corresponding search space. Deep generative models that learn directly from data without the need for domain insight are recently providing a way forward.
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