ProteinEngine: Empower LLM with domain knowledge for protein engineering

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 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, 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 ProteinEngine in augmenting the reliability and precision of deep learning in protein engineering tasks. Consequently, our findings highlight the potential of ProteinEngine to bride the disconnected tools for future research in the protein engineering domain.