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Gramacidin A channel

image size: 173.4KB
made with VMD

"If I could just get my hands on that protein!" Single molecule manipulation techniques like atomic force microscopy have brought us closer to this frequently expressed wish. These techniques, however, do not "see" the atomic level detail needed to relate mechanism to protein architectures. True, computational methods do illuminate the elusive protein structures, but are limited to static structures, or trajectories yielded by weeks-long simulations. Now, with the advent of inexpensive, high-performance computing, interactive manipulation of molecular dynamics simulations has become a reality. Linking advanced molecular graphics with ongoing molecular dynamics simulations, and utilizing a haptic device to connect forces from a user's hand with forces in the simulation, researchers can interact with "live" proteins. The new methodology is described in a recent publication and the figure shown here demonstrates a Cl- ion being pulled through a gramicidin A channel (see a 3.8mb Streaming Video).