Vaccines have not yet been able to address the combination of three major obstacles: molecular coupling failure between peptide and human leukocyte antigen protein (HLA‐II) molecule, failure to activate T‐cells, and the molecular polymorphism displayed by all pathogens. Planar electromagnetic fields found in protein systems may play a role in all three problems. These amino acid planes are universal, selective in nature, and able to generate long distance attraction toward their corresponding ligand. We propose three molecular mechanisms through which to engineer molecular pattern interaction toward the intelligent design of more effective vaccines.