General-purpose LLMs can satisfy simple local 3D constraints such as anchor fragments and pharmacophores, but their unoptimized poses dock much worse than those from specialized diffusion models.
A dual diffusion model enables 3d molecule generation and lead optimization based on target pockets.Nature Communications, 15(1):2657, Mar 2024
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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints
General-purpose LLMs can satisfy simple local 3D constraints such as anchor fragments and pharmacophores, but their unoptimized poses dock much worse than those from specialized diffusion models.