Highlights of our Work
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Our UIUC College of Engineering 2001 Open House event featured a simulation of the regulation of genetic expression in bacteria using NAMD and VMD. We showed a model of a repressor protein that shuts down an active DNA site by forcing the DNA to adopt a looped form. The combination of a detailed all-atom model for the protein with a coarse-grained model for the DNA loop helps us to reduce the computational time required to simulate the behavior of this protein-DNA system. With a second project we illustrated how through Interactive Molecular Dynamics (IMD) one can manipulate manually, with force feedback, simulated biomolecules for the purpose of drug design. IMD, via a haptic input device, relies on researchers' sense of touch in their quest to understand how biomolecules work. Finally, we presented BioCoRE, a collaborative research environment for structural biology within which researchers can visualize information, share resources and interact with each other and with structural biology tools via a common infrastructure and across time zones and continents.