Over the past few decades, machine learning (ML) has helped advance progress in a wide range of problems in computational biology and biochemistry, particularly towards understanding the structure and function of proteins. Similarly, in cheminformatics, ML is increasingly influencing pharmaceutical decision making and enabling novel drug design strategies. However, an area of great importance that requires further advances, likely involving significant innovations, is the understanding, prediction, and design of protein-protein and protein-ligand interactions. This Dagstuhl Seminar aims to connect the protein-ML and cheminformatics-ML communities and foster their communication with key experts in biology and chemistry. This seminar will allow us to discuss both theoretical and application-oriented ML topics in the context of protein-protein and protein-ligand interactions.