A novel caspase-3-specific inhibitory peptide and an agonistic peptide that binds to the Fas molecule were discovered using our computer screening strategy called the amino acid complement wave (ACW) method, which is based on the complementarities of interacting amino acids between comprehensive testing peptides and a target protein surface pocket. The precise binding configurations of the designed peptides on the three-dimensional (3D) structure of the target protein and the prediction of binding affinities (ΔG) are determined by the molecular docking program. A designed novel tetrapeptide inhibitor of caspase-3, Ac-DNLD-CHO, was revealed to have potent and specific inhibitory activity. When a designed Fas ligand mimic peptide (Fas reactive peptide-4, FRAP-4) was multimerized by carboxyl terminal linkages of polylysine branches (MAP), the octamer (FRAP-4)₈-MAP effectively induced apoptosis of human ovarian cancer cell line NOS4 cells. Thus the ACW method for structure-based design of optimized small peptides can be used to further develop small peptidomimetic and nonpeptidic organic forms into a new generation of effective pharmaceuticals.