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bioRxiv · 10.1101/2021.03.17.435706

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy

Guerler, A.·Baker, D.·van den Beek, M.·Bouvier, D.·Coraor, N.·Schatz, M. C.·Nekrutenko, A.
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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-CoV2s non-structural protein 3 (Nsp3). We also produced models of SARS-CoV2s 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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Guerler, A., Baker, D., van den Beek, M., Bouvier, D., Coraor, N., Schatz, M. C., Nekrutenko, A.. 2021-03-19. Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. https://doi.org/10.1101/2021.03.17.435706

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