arxivcs.LGcs.AIcs.CL2026-07-20
Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints
Thomas MacDougall, Maksim Kuznetsov, Roman Schutski, Rim Shayakhmetov, Maxim Malkov, Vladimir Aladinskiy, et al.
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-bas…