Ribosomal Kinetics and Concerted Motions from Nanoseconds to Seconds

1265-Plat Predicting Charged-Ligand Binding from Molecular Simulations David L. Mobley1, Gabriel J. Rocklin2. Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA, Biochemistry, University of Washington, Seattle, WA, USA. We seek to use molecular simulations to predict and understand protein-ligand interactions. Our approach uses so-called "alchemical" free energy calculations to quantitatively predict binding affinities. Here, we will discuss recent work on blind predictions of protein-ligand binding in a model binding site in cytochrome C peroxidase, as well as related work in other binding sites. We discuss the outcome of our predictions, what we learned, and the challenges facing computational methods in predicting biomolecular interactions. We also discuss ongoing related work in other binding sites, and implications of our work for binding studies more broadly.