Encoding the states of interacting proteins to facilitate biological pathways reconstruction

Alberto Termanini, Paolo Tieri, Claudio Franceschi

Research output: Contribution to journalArticlepeer-review


Background: In a systems biology perspective, protein-protein interactions (PPI) are encoded in machine-readable formats to avoid issues encountered in their retrieval for the reconstruction of comprehensive interaction maps and biological pathways. However, the information stored in electronic formats currently used doesn't allow a valid automatic reconstruction of biological pathways.Results: We propose a logical model of PPI that takes into account the "state" of proteins before and after the interaction. This information is necessary for proper reconstruction of the pathway.Conclusions: The adoption of the proposed model, which can be easily integrated into existing machine-readable formats used to store the PPI data, would facilitate the automatic or semi-automated reconstruction of biological pathways.Reviewers: This article was reviewed by Dr. Wen-Yu Chung (nominated by Kateryna Makova), Dr. Carl Herrmann (nominated by Dr. Purificación López-García) and Dr. Arcady Mushegian.

Original languageEnglish
Article number52
JournalBiology Direct
Publication statusPublished - Aug 13 2010

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology
  • Applied Mathematics
  • Modelling and Simulation
  • Ecology, Evolution, Behavior and Systematics


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