Theory of protein secondary structure and algorithm of its prediction

Abstract A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long‐range interactions between different regions, incorporating all these interactions in a single Ising‐like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α‐ and β‐structures for different residues in synthetic polypeptides, while long‐range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x‐ray structural data became available.