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Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

Anne Lopes 1 Sophie Sacquin-Mora 2 Viktoriya Dimitrova 3 Elodie Laine 3 Yann Ponty 4, 5 Alessandra Carbone 3, *
* Corresponding author
5 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : Protein-protein interactions (PPI) are at the heart of the molecular processes governing life and constitute an increasingly important target for drug design. Given their importance, it is vital to determine which protein interactions have functional relevance and to characterize the protein competition inherent to crowded environments, as the cytoplasm or the cellular organelles. We show that combining coarse-grain molecular cross-docking simulations and binding site predictions based on evolutionary sequence analysis is a viable route to identify true interacting partners for hundreds of proteins with a variate set of protein structures and interfaces. Also, we realize a large-scale analysis of protein binding promiscuity and provide a numerical characterization of partner competition and level of interaction strength for about 28000 false-partner interactions. Finally, we demonstrate that binding site prediction is useful to discriminate native partners, but also to scale up the approach to thousands of protein interactions. This study is based on the large computational effort made by thousands of internautes helping World Community Grid over a period of 7 months. The complete dataset issued by the computation and the analysis is released to the scientific community.
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Submitted on : Monday, October 21, 2013 - 11:06:45 AM
Last modification on : Thursday, January 13, 2022 - 5:02:45 AM

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Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, et al.. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. PLoS Computational Biology, Public Library of Science, 2013, 9 (12), pp.e1003369. ⟨10.1371/journal.pcbi.1003369⟩. ⟨hal-00875116⟩



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