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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: wiewiora rp. 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.
The dynamic conformational landscape of the protein methyltransferase SETD8.
Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M. Chen S, et al. Among authors: wiewiora rp. Elife. 2019 May 13;8:e45403. doi: 10.7554/eLife.45403. Elife. 2019. PMID: 31081496 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: wiewiora rp. 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.
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. Eastman P, et al. Among authors: wiewiora rp. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul. PLoS Comput Biol. 2017. PMID: 28746339 Free PMC article.