Methods of using overlapping peptides for the discovery of discontinuous epitopes, as vaccines, for drug design, for diagnostic purposes and for the elucidation of three-dimensional protein structure. Specifically, these methods can be used to map conformational epitopes using overlapping peptides. The methods are both complete, yet more specific than random phage libraries. They can also be used to develop DNA vaccines which exploit the concept of overlapping peptides in a variety of expression systems. Conformational epitopes prepared with these methods can be used for preparing antibodies, as components of diagnostic tools, and for elucidating three-dimensional protein structure.