We have developed an evolutionary computation approach to predict secondary structure motifs using some main amino acid physical-chemical properties. The prediction model will consist of rules that predict both the beginning and the end of the regions corresponding to a secondary structure state conformation (α-helix or β-strand). A study about propensities of each pair of amino acids in capping regions of α-helix and β-strand are also performed with a data set of 12,830 non-homologous and non-redundant protein sequences. © 2011 ACM.