Searching in protein state space

  • Authors:

  • Dietmar Seipel;Jörg Schultz

  • Affiliations:

  • Department of Computer Science, University of Würzburg, Würzburg, Germany;Department of Bioinformatics, Biozentrum, University of Würzburg, Würzburg, Germany

  • Venue:
  • INAP'09 Proceedings of the 18th international conference on Applications of declarative programming and knowledge management
  • Year:
  • 2009

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Abstract

The increasing complexity of protein interaction networks makes their manual analysis infeasible. Signal transduction processes pose a specific challenge, as each protein can perform different functions, depending on its state. Here, we present a PROLOG and XML based system which explores the protein state space. Starting with state based information about the function of single proteins, the system searches for all biologically reasonable states that can be reached from the starting point. As facts of general molecular biology have been integrated, novel reasonable states, not encoded in the starting set, can be reached. Furthermore, the influence of modifications like mutations or additions of further proteins can be explored. Thus, the system could direct experiments and allow to predict their outcome.