A new quantitative criterion to distinguish between alpha/beta and alpha+beta proteins (domains)

FEBS Lett. 1998 Nov 27;440(1-2):153-7. doi: 10.1016/s0014-5793(98)01433-1.

Abstract

According to the statistical analysis, it is shown that the differences of the content of alpha-helix and beta-strand between alpha/beta and alpha+beta proteins are of statistical significance. Based on the secondary structure content and the percentage of parallel or anti-parallel strands, any mixed alphabeta protein can be represented by a point in a three-dimensional prism. The distribution of the mapping points for 79 mixed alphabeta proteins (domains), of which 26 are class alpha/beta and 53 are class alpha+beta, shows that the two kinds of points are situated at distinct regions roughly. A new quantitative criterion based on the Fisher discriminant algorithm is proposed to distinguish between the alpha/beta and alpha+beta proteins (domains). Of the 79 proteins 77 are correctly classified (97.5%). As a stringent cross-validation test, the jackknife test shows that of the 79 proteins 77 are correctly classified. The jackknife test accuracy is still 97.5%. These figures indicate the self-consistence and the extrapolating effectiveness of the new quantitative criterion. Applying the new criterion to reclassify the alpha/beta and alpha+beta proteins (domains) in SCOP is also discussed. It is hoped that the new quantitative criterion will be useful for the development of protein classification databases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Data Interpretation, Statistical
  • Databases, Factual
  • Humans
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Proteins / classification
  • Sensitivity and Specificity

Substances

  • Proteins