Pseudoreceptor modeling allows the construction of a receptor surrogate for a structurally uncharacterized bioregulator (an enzyme or receptor) based on the structures of known ligand molecules. Although, in general, a pseudoreceptor and its natural counterpart will bear little structural resemblance, they should accommodate a series of ligand molecules in a relatively similar binding sense. A pseudoreceptor validated using a representative series of ligand molecules may subsequently be used to estimate relative free energies for binding for novel ligand molecules. A pseudoreceptor-modeling concept developed at our laboratory allows the generation of a three-dimensional peptidic receptor model (a miniprotein) about any molecular framework of interest. The concept was validated by constructing pseudoreceptors for the enzyme human carbonic anhydrase, the dopaminergic receptor, and the beta(2)-adrenergic receptor. Predicted differences in free energy of ligand binding toward the pseudoreceptor, Delta(Delta G degrees(calc)), and experimental values determined toward the biological receptor, Delta(Delta G degrees(exp)), agree to within 0.6 and 1.2 kcal/mol.