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.
Interaction-constrained 3d molec- ular generation using a diffusion model enables structure-based pharmacophore model- ing for drug design.npj Drug Discovery, 3(1):8, Mar 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.