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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. ChemRxiv [Preprint]. 2020 Jul 29. doi: 10.26434/chemrxiv.12725465. ChemRxiv. 2020. Update in: J Chem Inf Model. 2020 Dec 28;60(12):5832-5852. doi: 10.1021/acs.jcim.0c01010 PMID: 33200117 Free PMC article. Updated. Preprint.
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: acharya a. bioRxiv [Preprint]. 2020 Sep 10:2020.09.07.286344. doi: 10.1101/2020.09.07.286344. bioRxiv. 2020. Update in: Chem Sci. 2020 Nov 26;12(4):1513-1527. doi: 10.1039/d0sc04942e PMID: 32935106 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. 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: acharya a. 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: acharya a. 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.
Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants.
Yu B, Roy Choudhury M, Yang X, Benoit SL, Womack E, Van Mouwerik Lyles K, Acharya A, Kumar A, Yang C, Pavlova A, Zhu M, Yuan Z, Gumbart JC, Boykin DW, Maier RJ, Eichenbaum Z, Wang B. Yu B, et al. Among authors: acharya a. ACS Infect Dis. 2022 Aug 12;8(8):1491-1508. doi: 10.1021/acsinfecdis.2c00121. Epub 2022 Jul 8. ACS Infect Dis. 2022. PMID: 35801980 Free PMC article.
1,323 results