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BMC Bioinformatics. 2010 Jul 31;11:407. doi: 10.1186/1471-2105-11-407.

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

Author information

1
School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.

Abstract

BACKGROUND:

Beta-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 beta-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 beta-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of beta-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 beta-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/.

PMID:
20673368
PMCID:
PMC2920885
DOI:
10.1186/1471-2105-11-407
[Indexed for MEDLINE]
Free PMC Article

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