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Open Access Research article

Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures

Petros Kountouris and Jonathan D Hirst*

Author Affiliations

School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK

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BMC Bioinformatics 2010, 11:407  doi:10.1186/1471-2105-11-407

Published: 31 July 2010

Abstract

Background

β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains.

Results

We have developed a novel method that predicts β-turns and their types using information from multiple sequence alignments, predicted secondary structures and, for the first time, predicted dihedral angles. Our method uses support vector machines, a supervised classification technique, and is trained and tested on three established datasets of 426, 547 and 823 protein chains. We achieve a Matthews correlation coefficient of up to 0.49, when predicting the location of β-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of β-turn types I, II, IV, VIII and "non-specific", achieving correlation coefficients up to 0.39, 0.33, 0.27, 0.14 and 0.38, respectively. Our results are more accurate than other methods.

Conclusions

We have created an accurate predictor of β-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/ webcite.