Combating Infection through Atomic-Scale Modeling of Unique Bacterial System
Combating infection has become increasingly difficult because bacteria are acquiring resistance at an incredible pace, and current approaches to antibiotic development are producing diminishing returns.
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. Molecular Dynamics (MD) simulations provide a means for generating novel structural data and elucidating a system's evolution between structurally characterized states. We use umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force to calculatie of the transmembrane potential mean force. Our project contributes to computer-aided antibiotic development through the consideration of lipid membrane bilayer.
- Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 2016;56(4):721-33. doi: 10.1021/acs.jcim.6b00022.