Large Language and Protein Assistant for Protein-Protein Interactions Prediction

Abstract

Predicting the types and affinities of protein-protein interactions (PPIs) is crucial for understanding biological processes and developing novel therapeutic approaches. While encoding proteins themselves is essential, PPI networks can also provide rich prior knowledge for these predictive tasks. However, existing methods oversimplify the problem of PPI prediction in a semi-supervised manner when utilizing PPI networks, limiting their practical application. Furthermore, how to effectively use the rich prior knowledge of PPI networks for novel proteins not present in the network remains an unexplored issue. Additionally, due to inflexible architectures, most of existing methods cannot handle complexes containing an flexible number of proteins. To overcome these limitations, we introduce LLaPA (Large Language and Protein Assistant), a multimodal large language model that integrates proteins and PPI networks. LLaPA offers a more rational approach to utilizing PPI networks for PPI prediction and can fully exploit the information of PPI networks for unseen proteins. Through natural language instructions, LLaPA can accept flexible number of protein sequences and has the potential to perform various protein tasks. Experiments show that LLaPA achieves state-of-the-art performance in multi-label PPI (mPPI) type prediction and is capable of predicting the binding affinity between multiple interacting proteins based on sequence data.