Multiscale graph equivariant diffusion model for 3D molecule design

Three-dimensional molecular generation is critical in drug design. However, current methods often rely on point clouds or oversimplified interaction models, limiting their ability to accurately represent molecular structures. To address these challenges, this paper proposes the multiscale graph equivariant diffusion model for 3D molecule design (MD3MD). MD3MD partitions molecular conformations into multiscale graphs, assigning different weights to capture atomic interactions across scales. This framework guides the diffusion process, enabling high-quality 3D molecular generation. Experimental results demonstrate that MD3MD excels in both unconditional and conditional generation tasks, producing diverse, stable, and innovative molecules that meet specified conditions. Visualization highlights MD3MD’s ability to learn domain-specific patterns and generate molecules distinct from existing datasets while maintaining distributional consistency. By effectively exploring chemical space, MD3MD surpasses previous methods in generating innovative and chemically diverse molecules, offering a notable advancement in the field of molecular design.