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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: bhowmik d. 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.
Deep clustering of protein folding simulations.
Bhowmik D, Gao S, Young MT, Ramanathan A. Bhowmik D, et al. BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):484. doi: 10.1186/s12859-018-2507-5. BMC Bioinformatics. 2018. PMID: 30577777 Free PMC article.
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: bhowmik d. 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.
Adaptive language model training for molecular design.
Blanchard AE, Bhowmik D, Fox Z, Gounley J, Glaser J, Akpa BS, Irle S. Blanchard AE, et al. Among authors: bhowmik d. J Cheminform. 2023 Jun 8;15(1):59. doi: 10.1186/s13321-023-00719-7. J Cheminform. 2023. PMID: 37291633 Free PMC article.
Language models for the prediction of SARS-CoV-2 inhibitors.
Blanchard AE, Gounley J, Bhowmik D, Chandra Shekar M, Lyngaas I, Gao S, Yin J, Tsaris A, Wang F, Glaser J. Blanchard AE, et al. Among authors: bhowmik d. Int J High Perform Comput Appl. 2022 Nov;36(5-6):587-602. doi: 10.1177/10943420221121804. Int J High Perform Comput Appl. 2022. PMID: 38603308 Free PMC article.
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites.
Cho E, Rosa M, Anjum R, Mehmood S, Soban M, Mujtaba M, Bux K, Moin ST, Tanweer M, Dantu S, Pandini A, Yin J, Ma H, Ramanathan A, Islam B, Mey ASJS, Bhowmik D, Haider S. Cho E, et al. Among authors: bhowmik d. J Chem Inf Model. 2021 Jun 28;61(6):3058-3073. doi: 10.1021/acs.jcim.1c00449. Epub 2021 Jun 14. J Chem Inf Model. 2021. PMID: 34124899
The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases.
Olehnovics E, Yin J, Pérez A, De Fabritiis G, Bonomo RA, Bhowmik D, Haider S. Olehnovics E, et al. Among authors: bhowmik d. Front Microbiol. 2021 Sep 21;12:720991. doi: 10.3389/fmicb.2021.720991. eCollection 2021. Front Microbiol. 2021. PMID: 34621251 Free PMC article.
486 results