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Prediction of the location and type of β-turns in proteins using neural networks

Published online by Cambridge University Press:  01 May 1999

ADRIAN J. SHEPHERD
Affiliation:
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
DENISE GORSE
Affiliation:
Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
JANET M. THORNTON
Affiliation:
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Abstract

A neural network has been used to predict both the location and the type of β-turns in a set of 300 nonhomologous protein domains. A substantial improvement in prediction accuracy compared with previous methods has been achieved by incorporating secondary structure information in the input data. The total percentage of residues correctly classified as β-turn or not-β-turn is around 75% with predicted secondary structure information. More significantly, the method gives a Matthews correlation coefficient (MCC) of around 0.35, compared with a typical MCC of around 0.20 using other β-turn prediction methods. Our method also distinguishes the two most numerous and well-defined types of β-turn, types I and II, with a significant level of accuracy (MCCs 0.22 and 0.26, respectively).

Type
Research Article
Copyright
1999 The Protein Society

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