Antibiotics are small molecules used to treat infections worldwide. These molecules interfere with metabolic processes inside bacteria, thereby killing bacterial cells. Bacteria have developed many defense mechanisms to cope with antibiotics, including simply pumping them out of the cell using small transport proteins. EmrE is one such transport protein, found in E. coli that pumps out many different antibiotic molecules by using protons as an energy source. Together with Susan Rempe from Sandia National Laboratories in Albuquerque, we developed an atomic model for the transporter using interactive MDFF. Through extensive simulation and analysis performed in VMD, we determined the specific parts of the EmrE transport protein that couple together transport and protonation, which might lead to the development of antibiotics that can break the transporter. Read more about this study in the Proceedings of the National Academy of Sciences, and its companion commentary written by Jana Shen from the University of Maryland.