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.
Steering semi-flexible molecular diffusion model for structure-based drug design with reinforcement learning.Science Advances, 12(16):eady9955, 2026
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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.