Specific interactions of simple molecules produce phenomena of increasing complexity, culminating with the finely tuned biological mechanisms making life possible. Understanding the structure and dynamics of these molecules key to shed light on their function and malfunction in an organism. To this end, we develop and apply methods leveraging on molecular dynamics simulations, deep learning, graph theory and optimization techniques. Our current research focuses on the development and applications of methods for data fusion, protein-protein docking and characterization of protein conformational space.