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Searching in Protein State Space

  • Dietmar Seipel
  • Jörg Schultz
Conference paper
  • 249 Downloads
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6547)

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.

Keywords

Logic Programming Protein Interaction Network System Biology Markup Language Computation Tree Logic Signal Transduction Process 
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 2011

Authors and Affiliations

  • Dietmar Seipel
    • 1
  • Jörg Schultz
    • 2
  1. 1.Department of Computer ScienceUniversity of WürzburgWürzburgGermany
  2. 2.Department of Bioinformatics, BiozentrumUniversity of WürzburgWürzburgGermany

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