UC San Diego

Rational drug design has been revolutionized by computational methods such as molecular dynamics (MD) simulations and virtual screening. From both the methods development and the application standpoints, the entry of computation into chemistry has greatly changed how biophysics and medicinal chemistry are approached. First, we have developed an interactive platform on which a broader array of scientists can efficiently run molecular dynamics simulations, presenting an opportunity for a more rigorous and more accessible approach to utilizing this method. Second, virtual screening has allowed us to foray into the design of a protein-protein inhibitor for a polymeric form of IκB kinase alpha. And third, the application of molecular dynamics simulations has aided us in understanding the dynamics of proteins. Through MD, our studies on NF-κB-inducing kinase have given us insight into the interplay of interactions among its catalytic domains and revealed a possible allosteric site.