The study of intermolecular interactions is a fundamental research subject in biology. Here we report on the development of a quantitative structure‐based affinity scoring method for peptide–protein complexes, named PepScope. The method operates on the basis of a highly specific force field function (CHARMM) that is applied to all‐atom structural representations of peptide–receptor complexes. Peptide side‐chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. A de novo approach to estimate dehydration energies was developed, based on the simulation of individual amino acids in a solvent box filled with explicit water molecules. Transferability of the method was demonstrated by its application to the hydrophobic HLA‐A2 and ‐A24 receptors, the polar HLA‐A1, and the sterically ruled HLA‐B7 receptor. A combined theoretical and experimental study on 39 anchor substitutions in FxSKQYMTx/HLA‐A2 and ‐A24 complexes indicated a prediction accuracy of about two thirds of a log‐unit in Kd. Analysis of free energy contributions identified a great role of desolvation and conformational strain effects in establishing a given specificity profile. Interestingly, the method rightly predicted that most anchor profiles are less specific than so far assumed. This suggests that many potential T‐cell epitopes could be missed with current prediction methods. The results presented in this work may therefore significantly affect T‐cell epitope discovery programs applied in the field of peptide vaccine development. Proteins 2005. © 2004 Wiley‐Liss, Inc.