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NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

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  • Bent Petersen
  • Claus Lundegaard
  • Thomas Nordahl Petersen

Abstract

: β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC = 0.50, Qtotal = 82.1%, sensitivity = 75.6%, PPV = 68.8% and AUC = 0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17 – 0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. Conclusion: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.

Suggested Citation

  • Bent Petersen & Claus Lundegaard & Thomas Nordahl Petersen, 2010. "NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-9, November.
  • Handle: RePEc:plo:pone00:0015079
    DOI: 10.1371/journal.pone.0015079
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    Cited by:

    1. Harinder Singh & Sandeep Singh & Gajendra P S Raghava, 2014. "Evaluation of Protein Dihedral Angle Prediction Methods," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-9, August.

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