Prediction of beta-turn in protein using E-SSpred and support vector machine

Protein J. 2009 May;28(3-4):175-81. doi: 10.1007/s10930-009-9181-4.

Abstract

Beta-turn is a secondary protein structure type that plays an important role in protein configuration and function. Here, we introduced an approach of beta-turn prediction that used the support vector machine (SVM) algorithm combined with predicted secondary structure information. The secondary structure information was obtained by using E-SSpred, a new secondary protein structure prediction method. A 7-fold cross validation based on the benchmark dataset of 426 non-homologous protein chains was used to evaluate the performance of our method. The prediction results broke the 80% Q (total) barrier and achieved Q (total) = 80.9%, MCC = 0.44, and Q (predicted) higher 0.9% when compared with the best method. The results in our research are coincident with the conclusion that beta-turn prediction accuracy can be improved by inclusion of secondary structure information.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Artificial Intelligence*
  • Models, Chemical
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • ROC Curve
  • Reproducibility of Results
  • Software

Substances

  • Proteins