Secondary structural wobble: the limits of protein prediction accuracy

Biochem Biophys Res Commun. 2002 Jun 14;294(3):621-5. doi: 10.1016/S0006-291X(02)00545-4.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Humans
  • Models, Molecular*
  • Predictive Value of Tests
  • Protein Structure, Secondary*
  • Proteins / chemistry*

Substances

  • Proteins