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Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine.
ACS Cent Sci. 2022 Aug 24;8(8):1218-1228. doi: 10.1021/acscentsci.2c00565. Epub 2022 Aug 3.
ACS Cent Sci. 2022.
PMID: 36032773
Free PMC article.
Toward empirical force fields that match experimental observables.
Fröhlking T, Bernetti M, Calonaci N, Bussi G.
Fröhlking T, et al.
J Chem Phys. 2020 Jun 21;152(23):230902. doi: 10.1063/5.0011346.
J Chem Phys. 2020.
PMID: 32571067
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Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.
Mlýnský V, Janeček M, Kührová P, Fröhlking T, Otyepka M, Bussi G, Banáš P, Šponer J.
Mlýnský V, et al. Among authors: frohlking t.
J Chem Theory Comput. 2022 Apr 12;18(4):2642-2656. doi: 10.1021/acs.jctc.1c01222. Epub 2022 Apr 1.
J Chem Theory Comput. 2022.
PMID: 35363478
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Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.
Fröhlking T, Mlýnský V, Janeček M, Kührová P, Krepl M, Banáš P, Šponer J, Bussi G.
Fröhlking T, et al.
J Chem Theory Comput. 2022 Jul 12;18(7):4490-4502. doi: 10.1021/acs.jctc.2c00200. Epub 2022 Jun 14.
J Chem Theory Comput. 2022.
PMID: 35699952
Free PMC article.
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Deep learning path-like collective variable for enhanced sampling molecular dynamics.
Fröhlking T, Bonati L, Rizzi V, Gervasio FL.
Fröhlking T, et al.
J Chem Phys. 2024 May 7;160(17):174109. doi: 10.1063/5.0202156.
J Chem Phys. 2024.
PMID: 38748013
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Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations.
Gilardoni I, Fröhlking T, Bussi G.
Gilardoni I, et al. Among authors: frohlking t.
J Phys Chem Lett. 2024 Feb 8;15(5):1204-1210. doi: 10.1021/acs.jpclett.3c03423. Epub 2024 Jan 25.
J Phys Chem Lett. 2024.
PMID: 38272001
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Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data.
Fröhlking T, Bernetti M, Bussi G.
Fröhlking T, et al.
J Chem Phys. 2023 Jun 7;158(21):214120. doi: 10.1063/5.0151163.
J Chem Phys. 2023.
PMID: 37272569
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