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Page 1
SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines.
Bowen JE, Park YJ, Stewart C, Brown JT, Sharkey WK, Walls AC, Joshi A, Sprouse KR, McCallum M, Tortorici MA, Franko NM, Logue JK, Mazzitelli IG, Nguyen AW, Silva RP, Huang Y, Low JS, Jerak J, Tiles SW, Ahmed K, Shariq A, Dan JM, Zhang Z, Weiskopf D, Sette A, Snell G, Posavad CM, Iqbal NT, Geffner J, Bandera A, Gori A, Sallusto F, Maynard JA, Crotty S, Van Voorhis WC, Simmerling C, Grifantini R, Chu HY, Corti D, Veesler D. Bowen JE, et al. Among authors: simmerling c. Sci Immunol. 2022 Dec 23;7(78):eadf1421. doi: 10.1126/sciimmunol.adf1421. Epub 2022 Dec 23. Sci Immunol. 2022. PMID: 36356052 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: simmerling c. 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.
The need to implement FAIR principles in biomolecular simulations.
Amaro RE, Åqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, Cheatham TE 3rd, Cheung MS, Chipot C, Chong LT, Choudhary P, Cisneros GA, Clementi C, Collepardo-Guevara R, Coveney P, Covino R, Crawford TD, Dal Peraro M, de Groot BL, Delemotte L, De Vivo M, Essex JW, Fraternali F, Gao J, Gelpí JL, Gervasio FL, González-Nilo FD, Grubmüller H, Guenza MG, Guzman HV, Harris S, Head-Gordon T, Hernandez R, Hospital A, Huang N, Huang X, Hummer G, Iglesias-Fernández J, Jensen JH, Jha S, Jiao W, Jorgensen WL, Kamerlin SCL, Khalid S, Laughton C, Levitt M, Limongelli V, Lindahl E, Lindorff-Larsen K, Loverde S, Lundborg M, Luo YL, Luque FJ, Lynch CI, MacKerell AD Jr, Magistrato A, Marrink SJ, Martin H, McCammon JA, Merz K, Moliner V, Mulholland AJ, Murad S, Naganathan AN, Nangia S, Noe F, Noy A, Oláh J, O'Mara ML, Ondrechen MJ, Onuchic JN, Onufriev A, Osuna S, Palermo G, Panchenko AR, Pantano S, Parish C, Parrinello M, Perez A, Perez-Acle T, Perilla JR, Pettitt BM, Pietropaolo A, Piquemal JP, Poma AB, Praprotnik M, Ramos MJ, Ren P, Reuter N, Roitberg A, Rosta E, Rovira C, Roux B, Rothlisberger U, San… See abstract for full author list ➔ Amaro RE, et al. Among authors: simmerling c. Nat Methods. 2025 Apr;22(4):641-645. doi: 10.1038/s41592-025-02635-0. Nat Methods. 2025. PMID: 40175561 No abstract available.
InSty: A ProDy Module for Evaluating Protein Interactions and Stability.
Mikulska-Ruminska K, Krieger JM, Banerjee A, Cao X, Wu G, Bogetti AT, Zhang F, Simmerling C, Coutsias EA, Bahar I. Mikulska-Ruminska K, et al. Among authors: simmerling c. J Mol Biol. 2025 Aug 1;437(15):169009. doi: 10.1016/j.jmb.2025.169009. Epub 2025 Feb 13. J Mol Biol. 2025. PMID: 39954779
Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.
Linzer JT, Aminov E, Abdullah AS, Kirkup CE, Diaz Ventura RI, Bijoor VR, Jung J, Huang S, Tse CG, Álvarez Toucet E, Onghai HP, Ghosh AP, Grodzki AC, Haines ER, Iyer AS, Khalil MK, Leong AP, Neuhaus MA, Park J, Shahid A, Xie M, Ziembicki JM, Simmerling C, Nagan MC. Linzer JT, et al. Among authors: simmerling c. J Chem Inf Model. 2024 Aug 12;64(15):6092-6104. doi: 10.1021/acs.jcim.4c00756. Epub 2024 Jul 13. J Chem Inf Model. 2024. PMID: 39002142
110 results