Prediction of pi-turns in proteins using PSI-BLAST profiles and secondary structure information

Biochem Biophys Res Commun. 2006 Sep 1;347(3):574-80. doi: 10.1016/j.bbrc.2006.06.066. Epub 2006 Jun 21.

Abstract

Due to the structural and functional importance of tight turns, some methods have been proposed to predict gamma-turns, beta-turns, and alpha-turns in proteins. In the past, studies of pi-turns were made, but not a single prediction approach has been developed so far. It will be useful to develop a method for identifying pi-turns in a protein sequence. In this paper, the support vector machine (SVM) method has been introduced to predict pi-turns from the amino acid sequence. The training and testing of this approach is performed with a newly collected data set of 640 non-homologous protein chains containing 1931 pi-turns. Different sequence encoding schemes have been explored in order to investigate their effects on the prediction performance. With multiple sequence alignment and predicted secondary structure, the final SVM model yields a Matthews correlation coefficient (MCC) of 0.556 by a 7-fold cross-validation. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/piturn/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computational Biology / methods*
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • Proteins / chemistry*

Substances

  • Proteins