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Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence

  • Sauro Menchetti
  • Andrea Passerini
  • Paolo Frasconi
  • Claudia Andreini
  • Antonio Rosato
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3909)

Abstract

We describe and empirically evaluate machine learning methods for the prediction of zinc binding sites from protein sequences. We start by observing that a data set consisting of single residues as examples is affected by autocorrelation and we propose an ad-hoc remedy in which sequentially close pairs of candidate residues are classified as being jointly involved in the coordination of a zinc ion. We develop a kernel for this particular type of data that can handle variable length gaps between candidate coordinating residues. Our empirical evaluation on a data set of non redundant protein chains shows that explicit modeling the correlation between residues close in sequence allows us to gain a significant improvement in the prediction performance.

Keywords

Support Vector Machine Protein Data Bank Site Type Bonding State Metal Binding Site 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Sauro Menchetti
    • 1
  • Andrea Passerini
    • 1
  • Paolo Frasconi
    • 1
  • Claudia Andreini
    • 2
  • Antonio Rosato
    • 2
  1. 1.Machine Learning and Neural Networks Group, Dipartimento di Sistemi e InformaticaUniversità degli Studi di FirenzeItaly
  2. 2.Magnetic Resonance Center (CERM), Dipartimento di ChimicaUniversità degli Studi di FirenzeItaly

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