arXiv AI
Aug 28

AgentFold: Closed-Loop Agentic Search for Protein Folding Model Design

AgentFold is a multi‑agent framework that treats protein‑folding model design as a closed‑loop search over executable code variants. Starting from the ESMFold codebase, the agents generate hypotheses, modify and debug code, evaluate model variants, and store both successes and failures in structured memory, guided by an MCTS‑style policy that allocates GPU resources. In an engineering‑scale experiment, AgentFold explored about 80 variants using 5,000 GPU‑hours and 170 million LLM tokens, improving the best lDDT score by 7.5% over independent Codex proposals and outperforming a random‑search baseline, while also uncovering empirical design patterns such as the benefits of early, soft, learnable priors.

By Mingquan Liu, Jiangyu Chen, Hanqun Cao, Xujun Zhang, Pengsen Ma, Xiangru Tang, Shuting Jin, Zhuo Yang, Tianfan Fu, Fang Wu, Xiangxiang Zeng