FightAIDS@Home News Volume 4.1

The Relaxed Complex method will be used in many of the new experiments performed on the FightAIDS@Home grid. This wll allow us to evaluate potential drugs by docking fullyflexible versions of known and potential inhibitors against an ensemble of hundreds to thousands of different conformations of the target protein. In other words, we examine how well a potential drug binds to and blocks a massive collection of many of the different shapes that the drug target can sample as it wiggles and jiggles in a warm, watery environment). Proteins are very flexible polymers, and some potential drugs might not bind well to the average conformation that is represented in a particular crystal structure. Thus, by including the many different shapes that the target protein can display when we evaluate potential drugs, the drug design process can become more realistic and more accurate.