CIDD: Collaborative Intelligence for Structure-Based Drug Design Empowered by LLMs

Structure-guided molecular generation is pivotal in early-stage drug discovery, enabling the design of compounds tailored to specific protein targets. However, despite recent advances in 3D generative modeling, particularly in improving docking scores, these methods often produce rare and intrinsically irrational molecular structures that deviate from drug-like chemical space. To quantify this issue, we propose a novel metric, the Molecule Reasonable Ratio (MRR), which measures structural rationality and reveals a critical gap between existing models and real-world approved drugs. To address this, we introduce the Collaborative Intelligence Drug Design (CIDD) framework, the first approach to unify the 3D interaction modeling capabilities of generative models with the general knowledge and reasoning power of large language models (LLMs). By leveraging LLM-based Chain-of-Thought reasoning, CIDD generates molecules that not only bind effectively to protein pockets but also exhibit strong structural drug-likeness, rationality, and synthetic accessibility. On the CrossDocked2020 benchmark, CIDD consistently improves drug-likeness metrics, including QED, SA, and MRR, across different base generative models, while maintaining competitive binding affinity. Notably, it raises the combined success rate (balancing drug-likeness and binding) from 15.72% to 34.59%, more than doubling previous results. These findings demonstrate the value of integrating knowledge reasoning with geometric generation to advance AI-driven drug design.