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: | |
| 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: | |
| URI: | https://repository.cshl.edu/id/eprint/41020 |
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