The interaction between molecules is to a large extent decided by their specific conformations in space. Hence molecular shape analysis is one of the main challenges in structural biology, and geometric and topological methods are naturally important tools for this purpose. In this talk, we focus on two examples of using geometric/topological methods to capture geometric features of molecular shapes, and how such features are then used in protein docking and motif extraction applications. In the first example, we introduce a novel function called the \emph{Elevation} function defined over 2-manifolds, which is somewhat analog to the elevation on earth. The function is able to capture and describe meaningful features such as protrusions and cavities from input surfaces, and these features are crucial in identifying potential protein-protein docking configurations. In the second example, we use topological information from the distance field to help us identifying key motifs from families of protein structures.

Brief Bio: Yusu Wang is mainly interested in computational geometry, computational topology, as well as their applications in visualization, graphics and structural biology. She obtained her Ph.D degree from the Computer Science Dept. at Duke University in 2004. From 2004 - 2005, she was a postdoctoral fellow in the Geometric Computing Lab in the CS Dept. at Stanford University. She joined the Computer Science and Engineering Dept. at the Ohio State University in 2005. She received the DOE Early Career Award in 2006.