A proposed sequence of protein folding events in which the random coil, or denatured form, passes through three stages: the formation of fluctuating embyros, in which disconnected regions of secondary structure are formed; collapse of these regions into an intermediate compact structure or molten globule state that resembles the native conformation in overall outline but lacks the amino acid residue side chain interactions; and the tightening of the structure as the native conformation is assumed.

This scenario is contrasted with the subdomain model, in which highly organized subregions of a protein are formed before their final coming together in a process similar to a conformational change of the native protein, and the now abandoned jigsaw-puzzle model, in which partially folded intermediates are randomly formed and then progressively assume a greater degree of organization. In any of the folding models, the native protein conformation occupies a local energy minimum which may not be the lowest possible energy; in other words, the native structure is the result of its kinetic folding pathway. The thermodynamic model of protein structure, on the other hand, holds that the native conformation is the most stable and is, therefore, independent of the folding pathway.