PIDiff: Physics informed diffusion model for protein pocket-specific 3D molecular generation

Seungyeon Choi, Sangmin Seo, Byung Ju Kim, Chihyun Park, Sanghyun Park

Abstract: Highlights•Molecular structures binding to proteins must incorporate corresponding physicochemical principles.•We propose a 3D molecular generation model infused with the principle of minimizing binding free energy, crucial for binding.•This approach goes beyond learning empirical distributions of data, incorporating fundamental principles of protein-ligand binding.•Experiments from various perspectives demonstrate the potential of the proposed model for practical drug development.