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Page 1
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: trifan a. 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.
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: trifan 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.
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.
Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DGA, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman D, Mulholland A, Miller T 3rd, Jha S, Ramanathan A, Chong L, Amaro R. Dommer A, et al. Among authors: trifan a. bioRxiv [Preprint]. 2021 Nov 15:2021.11.12.468428. doi: 10.1101/2021.11.12.468428. bioRxiv. 2021. Update in: Int J High Perform Comput Appl. 2023 Jan;37(1):28-44. doi: 10.1177/10943420221128233 PMID: 34816263 Free PMC article. Updated. Preprint.
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.
Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DG, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman DM, Mulholland AJ, Miller T 3rd, Jha S, Ramanathan A, Chong L, Amaro RE. Dommer A, et al. Among authors: trifan a. Int J High Perform Comput Appl. 2023 Jan;37(1):28-44. doi: 10.1177/10943420221128233. Epub 2022 Oct 2. Int J High Perform Comput Appl. 2023. PMID: 36647365 Free PMC article.
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action.
Trifan A, Gorgun D, Salim M, Li Z, Brace A, Zvyagin M, Ma H, Clyde A, Clark D, Hardy DJ, Burnley T, Huang L, McCalpin J, Emani M, Yoo H, Yin J, Tsaris A, Subbiah V, Raza T, Liu J, Trebesch N, Wells G, Mysore V, Gibbs T, Phillips J, Chennubhotla SC, Foster I, Stevens R, Anandkumar A, Vishwanath V, Stone JE, Tajkhorshid E, A Harris S, Ramanathan A. Trifan A, et al. Among authors: a harris s. Int J High Perform Comput Appl. 2022 Nov;36(5-6):603-623. doi: 10.1177/10943420221113513. Epub 2022 Aug 5. Int J High Perform Comput Appl. 2022. PMID: 38464362 Free PMC article.
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.
Casalino L, Dommer AC, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti AT, Clyde A, Ma H, Lee H, Turilli M, Khalid S, Chong LT, Simmerling C, Hardy DJ, Maia JD, Phillips JC, Kurth T, Stern AC, Huang L, McCalpin JD, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. Casalino L, et al. Among authors: trifan a. Int J High Perform Comput Appl. 2021 Sep;35(5):432-451. doi: 10.1177/10943420211006452. Int J High Perform Comput Appl. 2021. PMID: 38603008 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: trifan a. 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.
Calmodulin complexes with brain and muscle creatine kinase peptides.
Sprenger J, Trifan A, Patel N, Vanderbeck A, Bredfelt J, Tajkhorshid E, Rowlett R, Lo Leggio L, Åkerfeldt KS, Linse S. Sprenger J, et al. Among authors: trifan a. Curr Res Struct Biol. 2021 May 19;3:121-132. doi: 10.1016/j.crstbi.2021.05.001. eCollection 2021. Curr Res Struct Biol. 2021. PMID: 34235492 Free PMC article.
Tailored Hydration for the Prevention of Contrast-Induced Acute Kidney Injury After Coronary Angiogram or PCI: A Systematic Review and Meta-Analysis.
Cossette F, Trifan A, Prévost-Marcotte G, Doolub G, So DF, Beaubien-Souligny W, Abou-Saleh D, Tanguay JF, Potter BJ, Ly HQ, Menkovic I, Cieza T, Avram R, Bastiany A, Marquis-Gravel G. Cossette F, et al. Among authors: trifan a. Am Heart J. 2025 Jan 3:S0002-8703(25)00002-X. doi: 10.1016/j.ahj.2025.01.002. Online ahead of print. Am Heart J. 2025. PMID: 39756561 Free article. Review.
305 results