Principles of Protein Structure - G. Schultz 1982

Secondary structure prediction from amino acid sequence
General remarks
Prediction as an analytical method

Modern Methods apparently make it possible to predict the structural Class of a protein. The prediction accuracy currently achieved allows a protein to be assigned to one of the five classes listed in Table 5.2. The Nature of the Secondary Structure in these classes is so distinct that they can be reliably distinguished from one another even with a prediction accuracy of 68% (Q^общ₃ in Table 6.5).

Predictions help identify new members within a group of related Proteins. In addition to determining the structural class, one can attempt to identify chains with a specific, already known topology. Applying the Chou and Fasman method [340] to Glutamate dehydrogenase, Bouton [386] identified two domains whose secondary structure is analogous to that of the nucleotide-binding domain in other previously studied dehydrogenases [254]. After establishing the overall STRUCTURE OF THE fragment, he found that its Amino Acid Sequence is homologous to that of one of these dehydrogenases (glyceraldehyde-3-phosphate dehydrogenase). This circumstance indicates a high "significance of similarity" (Sec. 9.6) and makes it possible to reveal an evolutionary relationship [387] reflected in the existence of a nucleotide-binding domain with the same chain topology. For the second of the considered domains, no Sequence Homology could be detected, although their secondary structures matched each other in character. In this case, the "significance" was too low to reveal topological similarity.

A similar approach was used by Argos [388] to study Ca²⁺-binding proteins; he demonstrated that predictions can facilitate the Determination of Amino acid sequences, particularly in ambiguous cases. Furthermore, using predictions, he attempted to locate the Ca²⁺-binding sites in the acyl carrier protein of E. coli fatty acid synthetase, as well as in the Proteins of the Blood Coagulation cascade.