The functions of biological macromolecules are dependent on their three-dimensional structures. Although the overall structure of these molecules are important for their functions, only a subset of residues are actively involved in a particular function mechanism. These functionally important residues are usually conserved as 3D substructures and/or motifs and are involved in molecular interactions as binding sites or catalytic mechanisms. In my research group, we have developed methods to identify and compare these 3D substructures in the structures of proteins and RNA. We have applied these methods to identify conserved functional sites in unrelated structures. In doing so, we can investigate the evolution of functional convergence in cases where similar motifs exist and carry out similar functions despite the overall structure being different with no detectable sequence or fold similarities. We also explore whether substructure searching methods could be deployed in applications such as drug development and synthetic biology.