The newly developed techniques of peptide libraries have drawn great interest in ligands selection, and also have provided us numerous facts in the fields of molecular recognition. Basing on these results, two new opinions on molecular recognition between macromolecules have been reviewed. First, noncovalent bonds formed between a few residues of two bonded macromolecules may make a major contribution to the total energy of binding. Second, short peptides bearing these critical residues can mimic the interaction of large proteins. Thus, by studying specific interactions of short peptides, some details of interaction of proteins may be discovered, and also some theoretical and experimental bases to the design of peptide medicines and vaccines, that may promote the study of supramolecular systems.