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 alpha-class/coil and beta-class/coil transitions but not direct alpha-class/beta-class transition. Propensity values representing the statistical occurrence of 20 amino acid residues in secondary structural wobbles are given.
Huang
Ji-Tao
JT
Department of Biochemistry, Tianjin Institute of Technology, Tianjin 300191, China. jthuang@mail.tjut.edu.cn
Wang
Ming-Tao
MT
D000818:Animals; D006801:Humans; D008958:Models, Molecular; D011237:Predictive Value of Tests; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins