El Agente F\'armaco: A Scalable AI Scientist for Drug Discovery

Abstract

Computational drug discovery offers a growing range of tools for proposing and evaluating molecules, but combining them and deciding what to do next still requires substantial expert effort. Here, we introduce El Agente F\'armaco, an AI scientist that uses modern large language model (LLM) technology to turn discovery goals expressed in everyday language into complex, scalable computational screening workflows. The agentic harness selects scientific tools, reviews their results, and adjusts subsequent steps to the target and the user's objectives. Our approach centers on a shared scientific memory: F\'armaco Atlas, which stores molecules, structures, and results together with their provenance -- a record of how they were obtained. The agent uses targeted database queries to retrieve the evidence needed for each decision. A single request can launch calculations for an entire collection of molecules, without requiring a separate LLM decision for every compound. This design limits the information the model must process as screening collections grow, while keeping the underlying results available for inspection and further analysis. The integrated tools support molecule generation, prediction of binding and molecular properties, and searches for compounds available for purchase. In a retrospective comparison with an expert-led campaign, the agent proposed chemically distinct candidates with competitive docking scores and higher calculated drug-likeness under explicitly imposed selection criteria. In a 22-task benchmark against plain tool calls and Codex, the agent achieved the highest observed mean model-judged score, with lower median cumulative token use and peak context. F\'armaco provides a foundation for flexible, scalable drug discovery workflows that connect scientific reasoning with an enduring, traceable record of computational work.