arXiv:2611.13651v1 Announce Type: cross Abstract: Drug discovery involves multiple interconnected research stages, including molecular design, property prediction, and virtual screening. These processes are characterized by complex workflows, interdependent computational tasks, and diverse specialized tools, placing substantial demands on the coordination of scientific models and computational resources. However, existing large language model (LLM)-based scientific agents still face challenges in autonomous planning of complex tasks, adaptive selection of specialized models, and reliable execution of multi-stage scientific computations, limiting their effectiveness in automating complex drug discovery workflows. To address these challenges, we propose DrugCoding, a scientific programming agent system that integrates scientific task planning, adaptive model routing, multi-agent collaboration, and programmatic tool execution. DrugCoding enables autonomous task planning and dynamic model adaptation for complex research objectives. It can flexibly invoke specialized scientific models, autonomously generate and execute code according to task requirements, and leverage multi-agent collaboration to support efficient execution and reliable validation of complex scientific tasks. To evaluate DrugCoding's performance in scientific tool invocation and multi-stage task execution, we conduct multi-turn tool-calling experiments across diverse language models and scientific tool interfaces. Experimental results demonstrate that DrugCoding achieves an average session-level Pass@1 of 97.35% on the full benchmark, outperforming the strongest baseline, Codex, by 9.24%. On the challenging subset, DrugCoding achieves 97.92%, exceeding the strongest baseline.