Fernando D. González-Nilo. Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.Three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were carried out on a series of 38 rubiscolins as δ opioid peptides using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Quantitative information on structure–activity relationships is provided for further rational development and direction of selective synthesis. All models were carried out over a training set including 30 peptides. The best CoMFA model included electrostatic and steric fields and had a moderate Q2 = 0.503. CoMSIA analysis surpassed the CoMFA results: the best CoMSIA model included only the hydrophobic field and had a Q2 = 0.661. In addition, this model predicted adequately the peptides contained in the test set. Our model identified that the potency of δ opioid activity of rubiscolin analogues essentially exhibited a significant relationship with local hydrophobic and hydrophilic characteristics of amino acids at positions 3, 4, 5, and 6.