Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints

Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules. While diffusion models have dominated as a leading paradigm for high-quality 3D molecule generation, LLM-based methods are rapidly emerging in molecular design and have shown competitive performance in pocket-conditioned molecular generation. However, their ability to reason about physics and 3D spatial environments is largely

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ethics.ai (20 July 2026), “Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints,” evidence record 12206, https://ethics.ai/record/12206 (originally published by arXiv cs.AI).

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