The interactome: Predicting the protein-protein interactions in cells

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland.
Cellular & Molecular Biology Letters (Impact Factor: 1.59). 11/2008; 14(1):1-22. DOI: 10.2478/s11658-008-0024-7
Source: PubMed


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.

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    • "et al., 2010). Computational prediction maps are fast and efficient to implement, and usually include satisfyingly large numbers of nodes and edges, but are necessarily imperfect because they use indirect information (Plewczynski and Ginalski, 2009). While high-throughput maps attempt to describe unbiased , systematic, and well-controlled data, they were initially more difficult to establish, although recent technological advances suggest that near completion can be reached within a few years for highly reliable, comprehensive protein-protein interaction and gene regulatory network maps for human (Venkatesan et al., 2009). "
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