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

Kountouris, Peter; Hirst, J.D.

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 b-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/.

Citation

Kountouris, P., & Hirst, J. (2010). Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11,

• Journal Article Type: Article
• Publication Date: Jan 1, 2010
• Deposit Date: Jan 26, 2011
• Publicly Available Date: Jan 26, 2011
• Journal: BMC Bioinformatics
• Electronic ISSN: 1471-2105
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 11
• Public URL: https://nottingham-repository.worktribe.com/output/1012802
• Publisher URL: http://dx.doi.org/10.1186/1471-2105-11-407
• Related Public URLs: http://comp.chem.nottingham.ac.uk/debt/