Superclusteroid: a Web tool dedicated to data processing of protein-protein interaction networks

Authors

  • Athina Ropodi Department of Informatics, University of Athens, GR-15784, Athens; Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, GR-11527, Athens
  • Nikolaos Sakkos Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, GR-11527, Athens
  • Charalampos Moschopoulos Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, GR-11527, Athens; 3Department of Computer Engineering & Informatics, University of Patras, GR-26500, Rio
  • George Magklaras The Biotechnology Centre of Oslo, University of Oslo, P.O. Box 1125 Blindern, 0317 Oslo
  • Sophia Kossida Biomedical Research Foundation of the Academy of Athens

DOI:

https://doi.org/10.14806/ej.17.2.239

Keywords:

protein-protein interactions, protein complexes, clustering algorithms

Abstract

The study of proteins and the interactions between them, known as Protein-Protein Interactions (PPI), is extremely important in interpreting all biological cellular functions. In this article, a new web tool called Superclusteroid is presented which can analyse PPI data, in order to detect protein complexes or characterise the functionality of unknown proteins. The tool is essentially an intuitive PPI data processing pipeline. It supports various input file formats and provides services such as clustering, PPI network visualisation and protein cluster function prediction. Each Superclusteroid service can be used in a sequential manner or on an individual basis. In order to assess the reliability of our tool to infer PPIs, the results of the tool were compared to already known MIPS database complexes and a case scenario is presented where a known protein complex is predicted and the functionality of some of its proteins is revealed.

Availability: Superclusteroid is freely available online at http://superclusteroid.uio.no/.

Author Biography

  • Sophia Kossida, Biomedical Research Foundation of the Academy of Athens
    Head of Bioinformatics & Medical Informatics Team
Embnet.journal 17.2

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Published

2011-10-20

Issue

Vol. 17 No. 2

Section

Research Papers

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