AutoBinder Agent: An MCP-Based Agent for End-to-End Protein Binder Design

Fukang Ge; Jiarui Zhu; Linjie Zhang; Haowen Xiao; Xiangcheng Bao; Fangnan Xie; Danyang Chen; Yanrui Lu; Yuting Wang; Ziqian Guan; Lin Gu; Jinhao Bi; Yingying Zhu

arXiv · 2602.00019

AutoBinder Agent: An MCP-Based Agent for End-to-End Protein Binder Design

Fukang Ge·Jiarui Zhu·Linjie Zhang·Haowen Xiao·Xiangcheng Bao·Fangnan Xie·Danyang Chen·Yanrui Lu·Yuting Wang·Ziqian Guan·Lin Gu·Jinhao Bi·Yingying Zhu

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Abstract

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

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Fukang Ge, Jiarui Zhu, Linjie Zhang, Haowen Xiao, Xiangcheng Bao, Fangnan Xie, Danyang Chen, Yanrui Lu, Yuting Wang, Ziqian Guan, Lin Gu, Jinhao Bi, Yingying Zhu. 2026-01-16. AutoBinder Agent: An MCP-Based Agent for End-to-End Protein Binder Design. https://arxiv.org/abs/2602.00019

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