This research develops approaches and strategies in Bioinformatics with explicit attention to applications of Computational Biology. The plan is to develop structural motifs retrieval into the protein database (PDB). The aim here is of exploiting the Generalized Hough Transform for the comparison and the search of structural similarity. Note that, if the searched structure is just a component of a protein (like a structural motif or a domain) the same method supports the detection and the statistical distribution of these components, possibly answering questions of permanence among different species and phylogenetic questions related to biological homology.