ProteinMCP: An Agentic AI Framework for Autonomous Protein Engineering

Authors

Xu, X., Feng, C., Zha, C., He, W., He, M., Xiao, B., Gao, X.

Abstract

Computational protein design is often constrained by slow, complex, inaccessible, and highly sophiscated and expert-dependent workflows that hinder its transferrability and generalization power for broader applications. We present ProteinMCP, an agentic AI framework designed to accelerate and democratize protein engineering. ProteinMCP automates end-to-end scientific tasks, delivering dramatic gains in efficiency; for instance, a comprehensive protein fitness modeling workflow was completed in just 11 minutes. This performance is achieved by an AI agent that intelligently orchestrates a unified ecosystem of 38 specialized tools, made accessible through a Model-Context-Protocol (MCP). A cornerstone of the framework is an automated pipeline that converts existing software into MCP-compliant servers, ensuring the platform is both powerful and perpetually extensible. We further demonstrate its capabilities through the successful autonomous design and selection of high-affinity de novo binders and therapeutic nanobodies. By removing technical barriers, ProteinMCP has the potential to shorten the design-build-test cycle and make advanced computational protein design accessible to the broader scientific community.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 15 Mar 2026.

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