Detection of Hydrophobic Clusters in Molecular Dynamics Protein Unfolding Simulations Using Association Rules

  • Paulo J. Azevedo
  • Cândida G. Silva
  • J. Rui Rodrigues
  • Nuno Loureiro-Ferreira
  • Rui M. M. Brito
Conference paper

DOI: 10.1007/11573067_33

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3745)
Cite this paper as:
Azevedo P.J., Silva C.G., Rodrigues J.R., Loureiro-Ferreira N., Brito R.M.M. (2005) Detection of Hydrophobic Clusters in Molecular Dynamics Protein Unfolding Simulations Using Association Rules. In: Oliveira J.L., Maojo V., Martín-Sánchez F., Pereira A.S. (eds) Biological and Medical Data Analysis. ISBMDA 2005. Lecture Notes in Computer Science, vol 3745. Springer, Berlin, Heidelberg

Abstract

One way of exploring protein unfolding events associated with the development of Amyloid diseases is through the use of multiple Molecular Dynamics Protein Unfolding Simulations. The analysis of the huge amount of data generated in these simulations is not a trivial task. In the present report, we demonstrate the use of Association Rules applied to the analysis of the variation profiles of the Solvent Accessible Surface Area of the 127 amino-acid residues of the protein Transthyretin, along multiple simulations. This allowed us to identify a set of 28 hydrophobic residues forming a hydrophobic cluster that might be essential in the unfolding and folding processes of Transthyretin.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Paulo J. Azevedo
    • 1
  • Cândida G. Silva
    • 2
  • J. Rui Rodrigues
    • 2
  • Nuno Loureiro-Ferreira
    • 2
  • Rui M. M. Brito
    • 2
    • 3
  1. 1.Departamento de InformáticaUniversidade do MinhoBragaPortugal
  2. 2.Centro de Neurociências de CoimbraUniversidade de CoimbraCoimbraPortugal
  3. 3.Departamento de Química, Faculdade de Ciências e TecnologiaUniversidade de CoimbraCoimbraPortugal

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