Primary amino acid content, and the geometry of the folded protein 3D structure are major parameters of protein function. During the course of evolution the protein 3D structure is more preserved than its primary sequence. Thus, analysis of protein structures is expected to lead to a deep insight into protein function. Recognition of a structural core common to a set of protein structures serves as a basic tool for the studies of protein evolution and classification, analysis of similar structural, motifs and functional binding sites, and for homology modeling and threading. In this chapter, we discuss several biologically related computational aspects of the multiple structure alignment and propose a method that provides solutions to these problems. Finally, we address the problem of structure-based multiple sequence alignment and propose an optimization method that unifies primary sequence and 3D structure information.