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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Available from: Dariusz Plewczynski, Nov 18, 2015
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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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    ABSTRACT: Solène Grosdidier1, Max Totrov2, Juan Fernández-Recio11Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain; 2Molsoft LLC, La Jolla, CA, USAAbstract: In recent years, protein–protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current efforts into the structural proteomics programs. Given that experimental determination of many protein–protein complex structures is highly challenging, and in the context of current high-performance computational capabilities, different computer tools are being developed to help in this task. Among them, computational docking aims to predict the structure of a protein–protein complex starting from the atomic coordinates of its individual components, and in recent years, a growing number of docking approaches are being reported with increased predictive capabilities. The improvement of speed and accuracy of these docking methods, together with the modeling of the interaction networks that regulate the most critical processes in a living organism, will be essential for computational proteomics. The ultimate goal is the rational design of drugs capable of specifically inhibiting or modifying protein–protein interactions of therapeutic significance. While rational design of protein–protein interaction inhibitors is at its very early stage, the first results are promising.Keywords: protein–protein interactions, drug design, protein docking, structural prediction, virtual ligand screening, hot-spots
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