Abstract
Backgroundβ-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.ResultsWe 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.ConclusionsWe 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/.
Highlights
Secondary structure can provide important information about three-dimensional protein structure
The effect of the input scheme Before optimising the support vector machines (SVMs) classifiers, we tried different input schemes, which showed that the combination of evolutionary information (PSSMs), predicted secondary structures and predicted dihedral angles gives the most accurate predictions
In this article, we presented a method that predicts the location of b-turns and their types in a protein chain
Summary
Secondary structure can provide important information about three-dimensional protein structure. The predictive accuracy reached 80% for three-state prediction, where residues are divided into helix, strand and coil. Helices and strands are repetitive, regular structures, while the remaining residues, which can be tight turns, loops, bulges or random coil, are all classified as coil; they are non-repetitive, irregular secondary structures [7]. The helix and strand classes are structurally well-defined, the third class, coil, does not provide any detailed structural information. Further analysis of the local structure is necessary, such as prediction of backbone dihedral angles [5,8] and prediction of tight turns [9]
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