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255 results

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Page 1
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. 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.
Classical molecular dynamics.
Brooks CL 3rd, Case DA, Plimpton S, Roux B, van der Spoel D, Tajkhorshid E. Brooks CL 3rd, et al. Among authors: case da. J Chem Phys. 2021 Mar 14;154(10):100401. doi: 10.1063/5.0045455. J Chem Phys. 2021. PMID: 33722022 No abstract available.
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… See abstract for full author list ➔ Amaro RE, et al. Among authors: case da. Nat Methods. 2025 Apr;22(4):641-645. doi: 10.1038/s41592-025-02635-0. Nat Methods. 2025. PMID: 40175561 Free article. No abstract available.
Generalized Born Implicit Solvent Models for Biomolecules.
Onufriev AV, Case DA. Onufriev AV, et al. Among authors: case da. Annu Rev Biophys. 2019 May 6;48:275-296. doi: 10.1146/annurev-biophys-052118-115325. Epub 2019 Mar 11. Annu Rev Biophys. 2019. PMID: 30857399 Free PMC article. Review.
Force fields for protein simulations.
Ponder JW, Case DA. Ponder JW, et al. Among authors: case da. Adv Protein Chem. 2003;66:27-85. doi: 10.1016/s0065-3233(03)66002-x. Adv Protein Chem. 2003. PMID: 14631816 Review. No abstract available.
Molecular Dynamics Simulations of Macromolecular Crystals.
Cerutti DS, Case DA. Cerutti DS, et al. Among authors: case da. 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.
Recent Developments in Amber Biomolecular Simulations.
Case DA, Cerutti DS, Cruzeiro VWD, Darden TA, Duke RE, Ghazimirsaeed M, Giambaşu GM, Giese TJ, Götz AW, Harris JA, Kasavajhala K, Lee TS, Li Z, Lin C, Liu J, Miao Y, Salomon-Ferrrer R, Shen J, Snyder R, Swails J, Walker RC, Wang J, Wu X, Zeng J, Cheatham Iii TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM Jr. Case DA, et al. J Chem Inf Model. 2025 Aug 11;65(15):7835-7843. doi: 10.1021/acs.jcim.5c01063. Epub 2025 Jul 29. J Chem Inf Model. 2025. PMID: 40728386 Free PMC article.
255 results