The structure of a protein gives important information about its function and can be used for understanding the evolutionary relationships among proteins, predicting protein functions, and predicting protein folding. A structural motif is a compact 3D protein block referring to a small specific combination of secondary structural elements which appears in a variety of molecules. In this paper we present a comparison between few approaches for motif retrieval based on the Generalized Hough Transform (GHT). Performance comparisons, in terms of precision and computation time, are presented considering the retrieval of motifs composed by three to five SSs for more than 15 million searches. The approaches object of this study can be easily applied to the retrieval of greater blocks, up to protein domains, or even entire proteins.