We address the question-can we use experimental design methods to investigate peptide conformation and identify conformational parameters that may contribute more significantly to the potential energy than others? We used mutually orthogonal Latin square design to sample the conformational space of peptides and analysed the samples using analysis of variance. We examined the equality of the effect of the torsion angles on the conforinational potential energy. The results showed that different torsion angles contributed differently to the conformational energy. We are able to identify those parameters that may have to be more carefully considered in conformational studies of peptides. (C) 2004 Elsevier Inc. All rights reserved.