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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: jha s. 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.
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers.
Bhati AP, Wan S, Alfè D, Clyde AR, Bode M, Tan L, Titov M, Merzky A, Turilli M, Jha S, Highfield RR, Rocchia W, Scafuri N, Succi S, Kranzlmüller D, Mathias G, Wifling D, Donon Y, Di Meglio A, Vallecorsa S, Ma H, Trifan A, Ramanathan A, Brettin T, Partin A, Xia F, Duan X, Stevens R, Coveney PV. Bhati AP, et al. Among authors: jha s. Interface Focus. 2021 Oct 12;11(6):20210018. doi: 10.1098/rsfs.2021.0018. eCollection 2021 Dec 6. Interface Focus. 2021. PMID: 34956592 Free PMC article.
Extensible and Scalable Adaptive Sampling on Supercomputers.
Hruska E, Balasubramanian V, Lee H, Jha S, Clementi C. Hruska E, et al. Among authors: jha s. J Chem Theory Comput. 2020 Dec 8;16(12):7915-7925. doi: 10.1021/acs.jctc.0c00991. Epub 2020 Nov 10. J Chem Theory Comput. 2020. PMID: 33170696
High-throughput binding affinity calculations at extreme scales.
Dakka J, Turilli M, Wright DW, Zasada SJ, Balasubramanian V, Wan S, Coveney PV, Jha S. Dakka J, et al. Among authors: jha s. BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):482. doi: 10.1186/s12859-018-2506-6. BMC Bioinformatics. 2018. PMID: 30577753 Free PMC article.
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics.
Casalino L, Dommer A, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti A, Ma H, Lee H, Turilli M, Khalid S, Chong L, Simmerling C, Hardy DJ, Maia JDC, Phillips JC, Kurth T, Stern A, Huang L, McCalpin J, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. Casalino L, et al. Among authors: jha s. bioRxiv [Preprint]. 2020 Nov 20:2020.11.19.390187. doi: 10.1101/2020.11.19.390187. bioRxiv. 2020. PMID: 33236007 Free PMC article. Updated. Preprint.
Large-Scale Molecular Dynamics Simulations of Cellular Compartments.
Wilson E, Vant J, Layton J, Boyd R, Lee H, Turilli M, Hernández B, Wilkinson S, Jha S, Gupta C, Sarkar D, Singharoy A. Wilson E, et al. Among authors: jha s. Methods Mol Biol. 2021;2302:335-356. doi: 10.1007/978-1-0716-1394-8_18. Methods Mol Biol. 2021. PMID: 33877636
Adaptive distributed replica-exchange simulations.
Luckow A, Jha S, Kim J, Merzky A, Schnor B. Luckow A, et al. Among authors: jha s. Philos Trans A Math Phys Eng Sci. 2009 Jun 28;367(1897):2595-606. doi: 10.1098/rsta.2009.0051. Philos Trans A Math Phys Eng Sci. 2009. PMID: 19451113
1,996 results