International Symposium on Bioinformatics Research and Applications

ISBRA 2011: Bioinformatics Research and Applications pp 358-367

Prediction of DNA-Binding Propensity of Proteins by the Ball-Histogram Method

  • Andrea Szabóová
  • Ondřej Kuželka
  • Sergio Morales E.
  • Filip Železný
  • Jakub Tolar
Conference paper

DOI: 10.1007/978-3-642-21260-4_34

Volume 6674 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Szabóová A., Kuželka O., Morales E. S., Železný F., Tolar J. (2011) Prediction of DNA-Binding Propensity of Proteins by the Ball-Histogram Method. In: Chen J., Wang J., Zelikovsky A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science, vol 6674. Springer, Berlin, Heidelberg

Abstract

We contribute a novel, ball-histogram approach to DNA-binding propensity prediction of proteins. Unlike state-of-the-art methods based on constructing an ad-hoc set of features describing the charged patches of the proteins, the ball-histogram technique enables a systematic, Monte-Carlo exploration of the spatial distribution of charged amino acids, capturing joint probabilities of specified amino acids occurring in certain distances from each other. This exploration yields a model for the prediction of DNA binding propensity. We validate our method in prediction experiments, achieving favorable accuracies. Moreover, our method also provides interpretable features involving spatial distributions of selected amino acids.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Andrea Szabóová
    • 1
  • Ondřej Kuželka
    • 1
  • Sergio Morales E.
    • 2
  • Filip Železný
    • 1
  • Jakub Tolar
    • 3
  1. 1.Czech Technical UniversityPragueCzech Republic
  2. 2.Instituto Tecnológico de Costa Rica ITCRCosta Rica
  3. 3.University of MinnesotaMinneapolisUSA