In a collaboration with the Dill group at UCSF, I am working on the ab initio protein structure prediction of small proteins (< 100 amino acids) such as CMTI and endothelin. Starting with the low resolution end point structure of our collaborators' folding algorithms, I use molecular dynamics to perform high resolution conformational sampling in search of the native structure, which we predict to be at the global minimum of our force field. Although homology modelling and threading are postulated to be successful in overall fold prediction within the next decade, and despite the great promise shown by folding algorithms, these techniques clearly lack sufficient detail at the molecular level that will allow structure prediction to have significant practical application. Of interest are the b inding pockets and active sites, where small structural differences lead to notable change in protein activity. Given a successful two-step method that accurately determines the macro- and microscopic structures of proteins, the pharmaceutical industry will benefit tremendously in its efforts to produce therapeutic drugs that are needed to modify protein activity. The Computer Graphics Laboratory has proven to be a valuable tool in enabling me to better analyze my data. I frequently use the visualization software package MidasPlus to look at my protein structures. I have also used the hardware to run other applications that display the trajectories of my dynamics simulations. The CGL staff is a helpful resource as well with their programming expertise.
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