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

By Peter Kountouris, J.D. Hirst and University of Notitngham

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.\ud \ud 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.\ud \ud 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/

Publisher: BioMed Central Ltd
Year: 2010
OAI identifier: oai:eprints.nottingham.ac.uk:1426
Provided by: Nottingham ePrints

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