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Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
Guerler, Aysam Baker, Dannon van den Beek, Marius Gruening, Bjoern Bouvier, Dave Coraor, Nate Schatz, Michael C. Nekrutenko, Anton
Guerler, Aysam
Baker, Dannon
van den Beek, Marius
Gruening, Bjoern
Bouvier, Dave
Coraor, Nate
Schatz, Michael C.
Nekrutenko, Anton
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Pre-print
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2021-04-14
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Bioinformatics
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https://doi.org/10.1101/2021.03.17.435706
Abstract
Protein-protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein-protein interactions and produce high-quality multimeric structural models. Application of our method to the Human and Yeast genomes yield protein-protein interaction networks similar in quality to common experimental methods. We identified and modeled Human proteins likely to interact with the papain-like protease of SARS-CoV2’s non-structural protein 3 (Nsp3). We also produced models of SARS-CoV2’s spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor (MOG) and dipeptidyl peptidase-4 (DPP4). The presented method is capable of confidently identifying interactions while providing high-quality multimeric structural models for experimental validation. The interactome modeling pipeline is available at usegalaxy.org and usegalaxy.eu.
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