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The flexibility of ACE2 in the context of SARS-CoV-2 infection.
Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. Barros EP, et al. Among authors: simmerling c. Biophys J. 2021 Mar 16;120(6):1072-1084. doi: 10.1016/j.bpj.2020.10.036. Epub 2020 Nov 13. Biophys J. 2021. PMID: 33189680 Free PMC article.
MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.
Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: simmerling c. bioRxiv [Preprint]. 2023 Dec 14:2023.11.29.569310. doi: 10.1101/2023.11.29.569310. bioRxiv. 2023. Update in: Biophys J. 2024 Sep 3;123(17):2902-2909. doi: 10.1016/j.bpj.2024.05.011 PMID: 38077000 Free PMC article. Updated. Preprint.
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: simmerling c. 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.
Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket.
Fallon L, Belfon KAA, Raguette L, Wang Y, Stepanenko D, Cuomo A, Guerra J, Budhan S, Varghese S, Corbo CP, Rizzo RC, Simmerling C. Fallon L, et al. Among authors: simmerling c. J Am Chem Soc. 2021 Aug 4;143(30):11349-11360. doi: 10.1021/jacs.1c00556. Epub 2021 Jul 16. J Am Chem Soc. 2021. PMID: 34270232 Free PMC article.
GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses.
Kim SH, Kearns FL, Rosenfeld MA, Casalino L, Papanikolas MJ, Simmerling C, Amaro RE, Freeman R. Kim SH, et al. Among authors: simmerling c. ACS Cent Sci. 2022 Jan 26;8(1):22-42. doi: 10.1021/acscentsci.1c01080. Epub 2021 Dec 15. ACS Cent Sci. 2022. PMID: 35106370 Free PMC article.
AmberTools.
Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O'Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE 3rd, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM Jr. Case DA, et al. Among authors: simmerling c. J Chem Inf Model. 2023 Oct 23;63(20):6183-6191. doi: 10.1021/acs.jcim.3c01153. Epub 2023 Oct 8. J Chem Inf Model. 2023. PMID: 37805934 Free PMC article.
107 results