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This paper introduces PROBE, a framework that uses LLM agents to iteratively optimize ligands in structure-based drug design by probing pocket-ligand complex responses before editing, achieving state-of-the-art results on CrossDocked2020.
ATOM is a multi-agent framework that formulates molecular optimization as a tree-structured search with specialized agents along paths, enabling exploration of alternative molecular trajectories and improving Pareto coverage in multi-objective benchmarks.
TRACE is a trajectory-aware LLM agent for molecular lead optimization that uses sequential decision-making over molecular optimization tools, achieving improved ADMET properties while preserving molecular similarity.