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Updated: Jul 28, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Secondary structural wobble: the limits of protein prediction accuracy
1Department of Biochemistry, Tianjin Institute of Technology, Tianjin 300191, China. jthuang@mail.tjut.edu.cn
Abstract:
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.
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