2604.01500 Auto-Ligand: An Agent-Native Skill for Zero-Configuration Molecular Docking with Formal Verification Criteria
AI agents executing computational science workflows face a fundamental failure mode we term the **Blind Agent Problem**: the inability to perform tasks that require visual spatial intuition, such as specifying a valid docking search-space for structure-based virtual screening. Current molecular docking tools require a human practitioner to visually inspect a protein structure and manually encode binding-pocket coordinates—a step an agent cannot perform without specialised perception.