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Next challenges in protein–protein docking: from proteome to interactome and beyond

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Abstract Advances in biophysics and biochemistry have pushed back the limits for the structural characterization of biomolecular assemblies. Large efforts have been devoted to increase both resolution and accuracy of the methods, probe into the smallest biomolecules as well as the largest macromolecular machineries, unveil transient complexes along with dynamic interaction processes, and, lately, dissect whole organism interactomes using high‐throughput strategies. However, the atomic description of such interactions, rarely reached by large‐scale projects in structural biology, remains indispensable to fully understand the subtleties of the recognition process, measure the impact of a mutation or predict the effect of a drug binding to a complex. Mixing even a limited amount of experimental and/or bioinformatic data with modeling methods, such as macromolecular docking, presents a valuable strategy to predict the three‐dimensional structures of complexes. Recent developments indicate that the docking community is seething to tackle the greatest challenge of adding the structural dimension to interactomes. © 2011 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

Predicting three‐dimensional (3D) interactomes by docking. Starting from experimental structures or models of all (or a subset of expressed proteins) in an organism, cross‐docking followed by binding affinity prediction would ideally allow to predict an interactome, adding at the same time the structural dimension to it.

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Flexible multidomain HADDOCKing illustrated with the interleukin‐1 receptor and its antagonist, PDBid: 1IRA, experiencing a conformational change of 19.5 Å upon binding.58 The receptor (orange) is cut into domains at its hinge region. The docking is then performed on the artificially generated multibody system: two subdomains of the receptor and the ligand (blue).

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Schematic representation of the energy landscape of two different protein–protein complexes.

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