Prediction of protein interactions between pine and pine wood nematode using deep learning and multi-dimensional feature fusion

Pine Wilt Disease (PWD) is a devastating forest disease that has a serious impact on ecological balance ecological. Since the identification of plant-pathogen protein interactions (PPIs) is a critical step in understanding the pathogenic system of the pine wilt disease, this study proposes a Multi-feature Fusion Graph Attention Convolution (MFGAC-PPI) for predicting plant-pathogen PPIs based on deep learning. Compared with methods based on single-feature information, MFGAC-PPI obtains more 3D characterization information by utilizing AlphaFold and combining protein sequence features to extract multi-dimensional features via Transform with improved GCN. The performance of MFGAC-PPI was compared with the current representative methods of sequence-based, structure-based and hybrid characterization, demonstrating its superiority across all metrics. The experiments showed that learning multi-dimensional feature information effectively improved the ability of MFGAC-PPI in plant and pathogen PPI prediction tasks. Meanwhile, a pine wilt disease PPI network consisting of 2,688 interacting protein pairs was constructed based on MFGAC-PPI, which made it possible to systematically discover new disease resistance genes in pine trees and promoted the understanding of plant-pathogen interactions.