Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de-novo protein structure prediction

Proteins. 2008 May 1;71(2):950-9. doi: 10.1002/prot.21779.


Distinguishing native from non-native folds remains a challenging problem for protein structure prediction. We describe a method, SCA-distance scoring, based on results from statistical coupling analysis which discriminates between native and non-native folds produced by a de novo protein structure prediction method for four out of five test proteins. The method is particularly good at discriminating non-native folds which are close in RMSD to the true fold but contain a change in an internal structural element. SCA-distance scoring is a useful addition to the tools available for distinguishing native from non-native folds in protein structure prediction.

MeSH terms

  • Mathematical Computing
  • Models, Molecular
  • Protein Folding*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Sequence Alignment / methods*
  • Thioredoxins / chemistry


  • Proteins
  • Thioredoxins