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 underexplored. In this work, we systematically analyze whether current general-purpose LLMs are capable of navigating complex 3D constraints compared to established baselines such as specialized d...
| Authors | Thomas MacDougall, Maksim Kuznetsov, Roman Schutski et al. |
|---|---|
| Primary category | cs.LG |
| Published | 20 July 2026 |
| Last updated at source | 20 July 2026 |
Silytics shows public metadata from arXiv and links to the original. Information may be incomplete or out of date. Last refreshed 17 October 2026. Licenses and terms of the original apply to the work itself. Not financial, legal or professional advice.