Secondary structural wobble: the limits of protein prediction accuracy

At present, accuracies of secondary structural prediction scarcely go beyond 70–75%. Secondary structural comparison is carried out among sequence-identified proteins. The results show natural wobble between different secondary structural types is possible in homologous families, and the best prediction accuracy will rarely be 100%. Besides shortcoming of the prediction approaches, secondary structural wobble is found to be responsible for nearly all secondary structural prediction limits. Only average 73.2% of amino acid residue is conserved in secondary structural types. The wobble allows <f>α</f>-class/coil and <f>β</f>-class/coil transitions but not direct <f>α</f>-class/<f>β</f>-class transition. Propensity values representing the statistical occurrence of 20 amino acid residues in secondary structural wobbles are given. [Copyright &y& Elsevier]