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The interactome: Predicting the protein-protein interactions in cells

1Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland

© 2008 University of Wrocław, Poland. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. (CC BY-NC-ND 3.0)

Citation Information: Cellular and Molecular Biology Letters. Volume 14, Issue 1, Pages 1–22, ISSN (Online) 1689-1392, DOI: 10.2478/s11658-008-0024-7, December 2008

Publication History

Published Online:
2008-12-24

Abstract

The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.

Keywords: Protein-protein interactions; Protein complexes; Docking; PDB Database; Interactome; Protein interaction networks; Physical protein interactions

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