In the preceding paper, using ECEPP, including the effects of water, and the chain build-up procedure, we computed the low energy structures for GnRH and found that there were no distinct low energy structures or structures with high statistical weights. To attempt to deduce possible structures of GnRH that may bind to the GnRH receptor, we computed the low energy structures for GnRH peptides that have L- and D-amino acids substituting for Gly 6. The L-amino acid-substituted peptides (L-Ala and L-Val) have very low or no affinity for the receptor and on activity (release of FSH and LH) while the D-Ala-, D-Leu-, D-Trp- and D-Phe-substituted peptides have significantly higher relative affinities and activities than those for native GnRH; the D-Val-substituted peptide has about one-third of the affinity and activity as native GnRH. Unlike native GnRH, our computations suggest that both sets of peptides form well-defined structures in water: the L-amino acid-substituted peptides are predominantly α-helical while the D-amino acid-substituted peptides adopted E*A A A E D*(C*) A E C A(C*) and minor variants of these structures. By eliminating structures that lay in common to the D-Ala and L-Val peptides and further eliminating structures that differed between the D-Ala and D-Leu peptides, we reduced the number of possible distinct binding conformations to 254. Searching for structures among these 254 conformations that had relative statistical weights that paralleled their relative affinities, we found two candidate structures: D*E A A E C*A E C A and D*G A A E D*A E C G*, both of which have conformations for residues 3-9 that are similar to the computed most probable structures for the D-amino acid-substituted GnRH peptides in water.