The rapidly growing body of 3D protein structure data provides new opportunities to study the relation between protein structure and protein function. Local structure pattern of proteins has been the focus of recent efforts to link structural features found in proteins to protein function. In addition, structure patterns have demonstrated values in applications such as predicting protein-protein interaction, engineering proteins, and designing novel medicines. My thesis introduces graph-based representations of protein structure and new subgraph mining algorithms to identify recurring structure patterns common to a set of proteins. These techniques enable families of proteins exhibiting similar function to be analyzed for structural similarity. Previous approaches to protein local structure pattern discovery operate in a pairwise fashion and have prohibitive computational cost when scaled to families of proteins. The graph mining strategy is robust in the face of errors in the structure, and errors in the set of proteins thought to share a function. Two collaborations with domain experts at the UNC School of Pharmacy and the UNC Medical School demonstrate the utility of these techniques. The first is to predict the function of several newly characterized protein structures. The second is to identify conserved structural features in evolutionarily related proteins
