The monograph is devoted to the consideration of existing approaches to the study of the principles of molecular structural organization and the mechanism of protein coagulation into native conformation. The book consists of an introduction and four parts. The first part describes the bifurcation theory of the assembly of the polypeptide chain itself, the physical conformation theory and the method of a priori calculation of the spatial structure of the protein according to the known amino acid sequence .. In other parts, the conformational capabilities of simple peptides, complex oligopeptides and proteins are considered. The results of quantitative analysis of conformational states of a large number of peptides and low-molecular proteins. are presented. The author’s approach to solving the inverse structural problem, which allows purposefully designing sets of artificial analogues, the spatial structure of which selectively corresponds to low-energy, potentially biologically active conformations of a natural peptide, is presented.