Encoding the states of interacting proteins to facilitate biological pathways reconstruction

• Published in: Biology direct Vol. 5; no. 1; p. 52
• Main Authors: Termanini, Alberto, Tieri, Paolo, Franceschi, Claudio
• Format: Journal Article
• Language: English
• Published: London BioMed Central 13.08.2010; BioMed Central Ltd; BMC
• Subjects: Animals; Biology; Biomedical and Life Sciences; Colleges & universities; Computational biology; Humans; Life Sciences; Models, Theoretical; Protein Interaction Mapping - methods; Protein-protein interactions; Proteins; Proteins - metabolism; Signal Transduction - physiology; Statistical models; Italy; Class Residue; Class Protein; Class Diagram; Native Conformation; Biological Pathway
• ISSN: 1745-6150; 1745-6150
• DOI: 10.1186/1745-6150-5-52

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.