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SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome.
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. Zimmerman MI, et al. bioRxiv [Preprint]. 2020 Oct 7:2020.06.27.175430. doi: 10.1101/2020.06.27.175430. bioRxiv. 2020. Update in: Nat Chem. 2021 Jul;13(7):651-659. doi: 10.1038/s41557-021-00707-0. PMID: 32637963 Free PMC article. Updated. Preprint.
How to Run FAST Simulations.
Zimmerman MI, Bowman GR. Zimmerman MI, et al. Methods Enzymol. 2016;578:213-25. doi: 10.1016/bs.mie.2016.05.032. Epub 2016 Jun 16. Methods Enzymol. 2016. PMID: 27497168 Review.
The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA.
Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. Cubuk J, et al. Among authors: zimmerman mi. bioRxiv [Preprint]. 2020 Dec 21:2020.06.17.158121. doi: 10.1101/2020.06.17.158121. bioRxiv. 2020. Update in: Nat Commun. 2021 Mar 29;12(1):1936. doi: 10.1038/s41467-021-21953-3. PMID: 32587966 Free PMC article. Updated. Preprint.
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential.
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. Vithani N, et al. Among authors: zimmerman mi. bioRxiv [Preprint]. 2020 Dec 10:2020.12.10.420109. doi: 10.1101/2020.12.10.420109. bioRxiv. 2020. Update in: Biophys J. 2021 Jul 20;120(14):2880-2889. doi: 10.1016/j.bpj.2021.03.024. PMID: 33330873 Free PMC article. Updated. Preprint.
31 results