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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: cerutti ds. 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.
Molecular Dynamics Simulations of Macromolecular Crystals.
Cerutti DS, Case DA. Cerutti DS, et al. Wiley Interdiscip Rev Comput Mol Sci. 2019 Jul-Aug;9(4):e1402. doi: 10.1002/wcms.1402. Epub 2018 Nov 16. Wiley Interdiscip Rev Comput Mol Sci. 2019. PMID: 31662799 Free PMC article.
Peptide crystal simulations reveal hidden dynamics.
Janowski PA, Cerutti DS, Holton J, Case DA. Janowski PA, et al. Among authors: cerutti ds. J Am Chem Soc. 2013 May 29;135(21):7938-48. doi: 10.1021/ja401382y. Epub 2013 May 16. J Am Chem Soc. 2013. PMID: 23631449 Free PMC article.
Fast Implementation of the Nudged Elastic Band Method in AMBER.
Ghoreishi D, Cerutti DS, Fallon Z, Simmerling C, Roitberg AE. Ghoreishi D, et al. Among authors: cerutti ds. J Chem Theory Comput. 2019 Aug 13;15(8):4699-4707. doi: 10.1021/acs.jctc.9b00329. Epub 2019 Jul 31. J Chem Theory Comput. 2019. PMID: 31314523 Free PMC article.
29 results