The group of Theoretical Structural Biology at the Technical University of Berlin is led by Dr. Ariane Nunes Alves. One of our main interests is the development and application of computational methods to predict kinetic rates for protein-ligand binding and enzyme-substrate binding. Knowledge of binding pathways and fine tuning of kinetic rates can lead to better drugs and improved enzyme catalysis. The main methods we use to study binding kinetics are molecular dynamics simulations and machine learning.
Another main interest is to understand how crowded environments affect protein-ligand binding and enzyme catalysis. While experiments and simulations to characterize proteins are usually performed using low concentration of proteins, the environment inside cells is crowded with different macromolecules. Such environment may affect binding and catalysis through excluded volume effects and quinary interactions.