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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: ramanathan a. 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
Holliday Junctions Formed from Human Telomeric DNA.
Haider S, Li P, Khiali S, Munnur D, Ramanathan A, Parkinson GN. Haider S, et al. Among authors: ramanathan a. J Am Chem Soc. 2018 Nov 14;140(45):15366-15374. doi: 10.1021/jacs.8b08699. Epub 2018 Oct 30. J Am Chem Soc. 2018. PMID: 30376323
Deep clustering of protein folding simulations.
Bhowmik D, Gao S, Young MT, Ramanathan A. Bhowmik D, et al. Among authors: ramanathan a. BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):484. doi: 10.1186/s12859-018-2507-5. BMC Bioinformatics. 2018. PMID: 30577777 Free PMC article.
Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning.
Romero R, Ramanathan A, Yuen T, Bhowmik D, Mathew M, Munshi LB, Javaid S, Bloch M, Lizneva D, Rahimova A, Khan A, Taneja C, Kim SM, Sun L, New MI, Haider S, Zaidi M. Romero R, et al. Among authors: ramanathan a. Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5086-5095. doi: 10.1073/pnas.1818411116. Epub 2019 Feb 26. Proc Natl Acad Sci U S A. 2019. PMID: 30808805 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: ramanathan a. 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.
Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.
Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson CB, Head MS, Coates L, Louis JM, Bonnesen PV, Kovalevsky A. Kneller DW, et al. Among authors: ramanathan a. J Med Chem. 2021 Dec 9;64(23):17366-17383. doi: 10.1021/acs.jmedchem.1c01475. Epub 2021 Oct 27. J Med Chem. 2021. PMID: 34705466 Free PMC article.
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor.
Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. Clyde A, et al. Among authors: ramanathan a. J Chem Inf Model. 2022 Jan 10;62(1):116-128. doi: 10.1021/acs.jcim.1c00851. Epub 2021 Nov 18. J Chem Inf Model. 2022. PMID: 34793155 Free article.
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2.
Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. Joshi RP, et al. Among authors: ramanathan a. J Chem Inf Model. 2023 Mar 13;63(5):1438-1453. doi: 10.1021/acs.jcim.2c01377. Epub 2023 Feb 21. J Chem Inf Model. 2023. PMID: 36808989
426 results