Evaluating predictions of secondary structure in proteins

To learn how secondary structure assignments diverge during divergent evolution, pairs of proteins with solved crystal structures were aligned and their assignments compared as a function of evolutionary distance. Residues assigned in one structure to a helix or a strand are frequently paired with residues assigned in the other to a coil. However, residues assigned to a helix in one structure are almost never paired with residues assigned to a strand in the other. This suggests additional limitations to the "three state residue-by-residue" score commonly used to evaluate secondary structure predictions and suggests recommendations for how secondary structure predictions should be scored to assess accurately their value as starting points for modelling tertiary structure.