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Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen S, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Acharya A, et al. Among authors: gumbart jc. ChemRxiv [Preprint]. 2020 Jul 29. doi: 10.26434/chemrxiv.12725465. ChemRxiv. 2020. PMID: 33200117 Free PMC article. Updated. Preprint.
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
Acharya A, Agarwal R, Baker MB, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen SY, Coates L, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller DW, Kovalevsky A, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers DM, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Acharya A, et al. Among authors: gumbart jc. J Chem Inf Model. 2020 Dec 28;60(12):5832-5852. doi: 10.1021/acs.jcim.0c01010. Epub 2020 Dec 16. J Chem Inf Model. 2020. PMID: 33326239 Free PMC article.
Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.
Zhang Z, Ryoo D, Balusek C, Acharya A, Rydmark MO, Linke D, Gumbart JC. Zhang Z, et al. Among authors: gumbart jc. Biochim Biophys Acta Biomembr. 2021 Oct 1;1863(10):183662. doi: 10.1016/j.bbamem.2021.183662. Epub 2021 Jun 17. Biochim Biophys Acta Biomembr. 2021. PMID: 34097860 Free PMC article.
Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.
Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Pavlova A, et al. Among authors: gumbart jc. Chem Sci. 2020 Nov 26;12(4):1513-1527. doi: 10.1039/d0sc04942e. eCollection 2021 Jan 28. Chem Sci. 2020. PMID: 35356437 Free PMC article.
149 results