Research

Encoding the states of interacting proteins to facilitate biological pathways reconstruction

Alberto Termanini^1*†, Paolo Tieri^1,2† and Claudio Franceschi^1,2

• * Corresponding author: Alberto Termanini alberto.termanini@gmail.com

• † Equal contributors

Author Affiliations

¹ 'L. Galvani' Interdepartmental Center, University of Bologna, Via San Giacomo 12, 40126 Bologna, Italy

² Department of Experimental Pathology, University of Bologna, Via San Giacomo 12, 40126 Bologna, Italy

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Biology Direct 2010, 5:52 doi:10.1186/1745-6150-5-52

Published: 13 August 2010

Abstract

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.