Abstract
Machine learning for protein modeling faces significant challenges due to proteins' inherently dynamic nature, yet most graph-based machine learning methods rely solely on static structural information. Recently, the growing availability of molecular dynamics trajectories provides new opportunities for understanding the dynamic behavior of proteins; however, computational methods for utilizing this dynamic information remain limited. We propose a novel graph representation that integrates both static structural information and dynamic correlations from molecular dynamics trajectories, enabling more comprehensive modeling of proteins. By applying relational graph neural networks (RGNNs) to process this heterogeneous representation, we demonstrate significant improvements over structure-based approaches across three distinct tasks: atomic adaptability prediction, binding site detection, and binding affinity prediction. Our results validate that combining static and dynamic information provides complementary signals for understanding protein-ligand interactions, offering new possibilities for drug design and structural biology applications.