On the contrary, the interactions between peptide and Glu11 and Asn62 played a key role in orientation, suggesting that both the residues were obligatory during the binding of TP5 into the binding cleft. On the basis of Autodock3.0.5 method, a certain number of energy evaluations may converge to a correct energy minimum. That implies more members of the populations will be converged to the lowest energy conformation. Thus, if the energy evaluation is further increased, the system will be remained at the same conformation. According to the rule, the maximum number of energy evaluations was set to 100 million for the following calculations. Confirming the complex formation between TP5 and HLA-DR, we assessed the ability of HLA-DR to functionally recognize alanine LY2835219 substitutions of TP5 under the same parameters. The best complexes with the lowest binding energy and the same direction between peptides and the groove were used as the inputs for further minimization. In Table 2, the binding energy of TP5 binding to HLA-DR was the least value among six binding energies. This result means that the most stable complex of HLADR/ TP5 was formed. Remarkably, the substitution of Arg at position 1 considerably reduced the binding affinity. However, as shown in Fig. 6B, the alanine substitution of Arg stretched into the cleft deeply and bound to the same binding site with Glu11 and Asn62, which accounted for its obligatory nature for Arg at position 1 for actual interacting with the receptor. In contrast to this observation, the alanine substitution of Lys at position 2 reduced the binding affinity to the Oligomycin A minimum extent; the substitution failed to stretch into the same binding site containing Glu11 and Asn62 instead of projecting out the binding groove. In particular, the interactions of Arg and Lys with the binding sites ensured the occurrence of binding and the direction of the N-terminal of the peptide. Whereas, the alanine substitution of Val at position 4 reduced the binding affinity to the maximum extent and bound HLA-DR in a distinct manner from TP5, projecting out the cleft. The substitution of Asp and Tyr at positions 3 and 5 resulted in a moderate decrease of binding affinity and variant binding sites without Glu11. Interestingly, both the substitutions bound into the binding cleft. Examination of the docking results revealed that TP5 was predicted to be optimal for binding into the cleft within the MHC molecules. The role of TP5 in clinical treatment in immune system was well established, however, the refined mechanism of its action is not known in details. According to the main idea of immunomodulation, we suppose that it were obligatory for TP5 to form complex with MHC II before TP5 interacts with TCRs. For class II MHC molecules, they bound peptides with various length. More importantly, a tentative DR motif that governs the fine-specificity of antigen presentation had been well known recently.