ProtChatGPT: Towards Understanding Proteins with Hybrid Representation and Large Language Models

Protein research is crucial in various scientific disciplines, but understanding their intricate structure-function relationships remains challenging. Recent advancements in Large Language Models (LLMs) have significantly improved the comprehension of task-specific knowledge, suggesting the potential for specialized ChatGPT-like systems in protein research to aid fundamental investigations. In this work, we introduce ProtChatGPT, which aims to learn and understand protein structures using natural language. ProtChatGPT enables users to upload proteins, ask questions, and engage in interactive conversations to produce comprehensive answers. The system comprises multi-level protein encoding, protein-language alignment, and instruction tuning of LLMs. A protein first undergoes multiple protein encoders and PLP-former to produce multi-level hybrid protein embeddings, which are then aligned through a Protein Context Gating (PCG) module with contrastive learning, and projected by an adapter to conform with the LLM. The LLM finally combines user questions with projected protein embeddings to generate informative answers. Experiments show that ProtChatGPT can produce promising responses to proteins and the corresponding user questions. We hope that ProtChatGPT could form the basis for further exploration and application in protein research. Code and our pre-trained model will be publicly available.