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, Shank, Stephen D, Zehr, Jordan D, Schatz, Michael C, Nekrutenko, Anton (June 2023) Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. BMC Bioinformatics, 24 (1). p. 263. ISSN 1471-2105

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Abstract

BACKGROUND: 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. RESULTS: 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. We also produced models of SARS-CoV2's spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor and dipeptidyl peptidase-4. CONCLUSIONS: 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.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > annotation bioinformatics diseases & disorders bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > annotation > map annotation diseases & disorders > viral diseases diseases & disorders > viral diseases > coronavirus diseases & disorders > viral diseases > coronavirus > covid 19
CSHL Authors:	Schatz, Michael C.
Communities:	CSHL labs > Schatz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	23 June 2023
Date Deposited:	11 Oct 2023 13:36
Last Modified:	08 Jan 2024 21:05
PMCID:	PMC10288729
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41020

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