FoldX The FoldX method is also another popular alternative method for quickly estimating the importance of the interactions within a protein or protein complexes, also using an empirical forcefield . In the case of FoldX, we used the pssm command to estimate the effect of each of the 20 natural amino acids at each peptide position of the MHC class I protein-peptide complexes. Neighbors residues were allowed to move during the energy calculations, and only one run was done for each mutation (as suggested in the documentation). At the end of the calculations, the mutations were ranked based on the predicted ∆∆G energy scores. The method was also benchmarked in the context MHC class I protein-peptide complexes. [85]