Protein function, which is determined by sequence, structure, and other characteristics, plays a crucial role in an organism's performance. Existing protein function prediction methods mainly rely on sequence data and often ignore structural properties that are crucial for accurate prediction. Protein structure provides richer spatial and functional insights, which can significantly improve prediction accuracy. In this work, we propose a multi-modal protein function prediction model (MMPFP) that integrates protein sequence and structure information through the use of GCN, CNN, and Transformer models. We validate the model using the PDBest dataset, demonstrating that MMPFP outperforms traditional single-modal models in the molecular function (MF), biological process (BP), and cellular component (CC) prediction tasks. Specifically, MMPFP achieved AUPR scores of 0.693, 0.355, and 0.478; [Formula: see text] scores of 0.752, 0.629, and 0.691; and [Formula: see text] scores of 0.336, 0.488, and 0.459, showing a 3-5% improvement over single-modal models. Additionally, ablation studies confirm the effectiveness of the Transformer module within the GCN branch, further validating MMPFP's superior performance over existing methods. This multi-modal approach offers a more accurate and comprehensive framework for protein function prediction, addressing key limitations of current models.
