Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures
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 informati...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Published: |
BioMed Central Ltd
2010
|
| Online Access: | https://eprints.nottingham.ac.uk/1426/ |
| _version_ | 1848790603945476096 |
|---|---|
| author | Kountouris, Peter Hirst, J.D. |
| author_facet | Kountouris, Peter Hirst, J.D. |
| author_sort | Kountouris, Peter |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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/. |
| first_indexed | 2025-11-14T18:15:15Z |
| format | Article |
| id | nottingham-1426 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T18:15:15Z |
| publishDate | 2010 |
| publisher | BioMed Central Ltd |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-14262020-05-04T20:25:34Z https://eprints.nottingham.ac.uk/1426/ Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures Kountouris, Peter Hirst, J.D. 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/. BioMed Central Ltd 2010 Article PeerReviewed Kountouris, Peter and Hirst, J.D. (2010) Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11 . p. 407. ISSN 1471-2105 http://dx.doi.org/10.1186/1471-2105-11-407 |
| spellingShingle | Kountouris, Peter Hirst, J.D. Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| title | Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| title_full | Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| title_fullStr | Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| title_full_unstemmed | Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| title_short | Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| title_sort | predicting β-turns and their types using predicted backbone dihedral angles and secondary structures |
| url | https://eprints.nottingham.ac.uk/1426/ https://eprints.nottingham.ac.uk/1426/ |