ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering

TL;DR

ProteinEngine enhances large language models for protein engineering by integrating domain-specific tools and roles, significantly improving task accuracy and reliability through a human-centered, extensible platform validated by user studies.

Contribution

This work introduces ProteinEngine, a novel platform that integrates domain-specific tools with LLMs via API calls, enabling specialized protein engineering tasks with high extensibility.

Findings

ProteinEngine outperforms baseline models in protein engineering tasks.

User studies confirm improved reliability and precision.

Platform facilitates seamless integration of new algorithms.

Abstract

Large language models (LLMs) have garnered considerable attention for their proficiency in tackling intricate tasks, particularly leveraging their capacities for zero-shot and in-context learning. However, their utility has been predominantly restricted to general tasks due to an absence of domain-specific knowledge. This constraint becomes particularly pertinent in the realm of protein engineering, where specialized expertise is required for tasks such as protein function prediction, protein evolution analysis, and protein design, with a level of specialization that existing LLMs cannot furnish. In response to this challenge, we introduce \textsc{ProteinEngine}, a human-centered platform aimed at amplifying the capabilities of LLMs in protein engineering by seamlessly integrating a comprehensive range of relevant tools, packages, and software via API calls. Uniquely, \textsc{ProteinEngine} assigns three distinct roles to LLMs, facilitating efficient task delegation, specialized task resolution, and effective communication of results. This design fosters high extensibility and promotes the smooth incorporation of new algorithms, models, and features for future development. Extensive user studies, involving participants from both the AI and protein engineering communities across academia and industry, consistently validate the superiority of \textsc{ProteinEngine} in augmenting the reliability and precision of deep learning in protein engineering tasks. Consequently, our findings highlight the potential of \textsc{ProteinEngine} to bride the disconnected tools for future research in the protein engineering domain.