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Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC; COVID Moonshot Consortium‡; Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, Aschenbrenner JC, Balcomb BH, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Bilenko VA, Borden B, Boulet P, Bowman GR, Brewitz L, Brun J, Bvnbs S, Calmiano M, Carbery A, Carney DW, Cattermole E, Chang E, Chernyshenko E, Clyde A, Coffland JE, Cohen G, Cole JC, Contini A, Cox L, Croll TI, Cvitkovic M, De Jonghe S, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett LE, Eastman P, Erez N, Eyermann CJ, Fairhead M, Fate G, Fedorov O, Fernandes RS, Ferrins L, Foster R, Foster H, Fraisse L, Gabizon R, García-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen RC, Glinert I, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Haneef A, Hassell Hart S, Heer J, Henry M, Hill M, Horrell S, Huang QYJ, Huliak VD, Hurley MFD, Israely T, Jajack A, Jansen J, Jnoff E, Jochmans D, John T, Kaminow B, Kang L, Kantsadi AL, Kenny PW, Kiappes JL, Kinakh SO, Kovar B, Krojer T, La VNT, Laghnimi-Hahn S, Lefker BA, Levy H, Lithgo RM, Logvinenko IG, Lukacik P, Macdonald HB, MacLean … See abstract for full author list ➔ Boby ML, et al. Among authors: singh s. Science. 2023 Nov 10;382(6671):eabo7201. doi: 10.1126/science.abo7201. Epub 2023 Nov 10. Science. 2023. PMID: 37943932 Free PMC article.
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. Among authors: singh s. bioRxiv [Preprint]. 2020 Oct 7:2020.06.27.175430. doi: 10.1101/2020.06.27.175430. bioRxiv. 2020. PMID: 32637963 Free PMC article. Updated. Preprint.
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: singh s. Nat Commun. 2021 Mar 29;12(1):1936. doi: 10.1038/s41467-021-21953-3. Nat Commun. 2021. PMID: 33782395 Free PMC article.
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and 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. Among authors: singh s. Nat Chem. 2021 Jul;13(7):651-659. doi: 10.1038/s41557-021-00707-0. Epub 2021 May 24. Nat Chem. 2021. PMID: 34031561 Free PMC article.
A cryptic pocket in Ebola VP35 allosterically controls RNA binding.
Cruz MA, Frederick TE, Mallimadugula UL, Singh S, Vithani N, Zimmerman MI, Porter JR, Moeder KE, Amarasinghe GK, Bowman GR. Cruz MA, et al. Among authors: singh s. Nat Commun. 2022 Apr 27;13(1):2269. doi: 10.1038/s41467-022-29927-9. Nat Commun. 2022. PMID: 35477718 Free PMC article.
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