Bussi G - Search Results

1

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations.

Do TN, Carloni P, Varani G, Bussi G. Do TN, et al. Among authors: bussi g. J Chem Theory Comput. 2013 Mar 12;9(3):1720-30. doi: 10.1021/ct3009914. Epub 2013 Feb 22. J Chem Theory Comput. 2013. PMID: 26587630

2

Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering.

Dutta A, Tapio K, Suma A, Mostafa A, Kanehira Y, Carnevale V, Bussi G, Bald I. Dutta A, et al. Among authors: bussi g. Nanoscale. 2022 Nov 17;14(44):16467-16478. doi: 10.1039/d2nr03664a. Nanoscale. 2022. PMID: 36305892 Free PMC article.

3

Accurate multiple time step in biased molecular simulations.

Ferrarotti MJ, Bottaro S, Pérez-Villa A, Bussi G. Ferrarotti MJ, et al. Among authors: bussi g. J Chem Theory Comput. 2015 Jan 13;11(1):139-46. doi: 10.1021/ct5007086. Epub 2014 Dec 23. J Chem Theory Comput. 2015. PMID: 26574212

4

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P. Kührová P, et al. Among authors: bussi g. J Chem Theory Comput. 2016 Sep 13;12(9):4534-48. doi: 10.1021/acs.jctc.6b00300. Epub 2016 Aug 4. J Chem Theory Comput. 2016. PMID: 27438572 Free PMC article.

5

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement.

Cesari A, Gil-Ley A, Bussi G. Cesari A, et al. Among authors: bussi g. J Chem Theory Comput. 2016 Dec 13;12(12):6192-6200. doi: 10.1021/acs.jctc.6b00944. Epub 2016 Dec 5. J Chem Theory Comput. 2016. PMID: 27951677

6

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.

Pinamonti G, Zhao J, Condon DE, Paul F, Noè F, Turner DH, Bussi G. Pinamonti G, et al. Among authors: bussi g. J Chem Theory Comput. 2017 Feb 14;13(2):926-934. doi: 10.1021/acs.jctc.6b00982. Epub 2017 Jan 5. J Chem Theory Comput. 2017. PMID: 28001394 Free PMC article.

7

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

Islam B, Stadlbauer P, Gil-Ley A, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banas P, Otyepka M, Sponer J. Islam B, et al. Among authors: bussi g. J Chem Theory Comput. 2017 Jun 13;13(6):2458-2480. doi: 10.1021/acs.jctc.7b00226. Epub 2017 May 18. J Chem Theory Comput. 2017. PMID: 28475322 Free PMC article.

8

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P. Kührová P, et al. Among authors: bussi g. J Chem Theory Comput. 2019 May 14;15(5):3288-3305. doi: 10.1021/acs.jctc.8b00955. Epub 2019 Apr 2. J Chem Theory Comput. 2019. PMID: 30896943 Free PMC article.

9

Promoting transparency and reproducibility in enhanced molecular simulations.

PLUMED consortium. PLUMED consortium. Nat Methods. 2019 Aug;16(8):670-673. doi: 10.1038/s41592-019-0506-8. Nat Methods. 2019. PMID: 31363226 Free article. No abstract available.

10

Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides.

Mlýnský V, Kührová P, Kühr T, Otyepka M, Bussi G, Banáš P, Šponer J. Mlýnský V, et al. Among authors: bussi g. J Chem Theory Comput. 2020 Jun 9;16(6):3936-3946. doi: 10.1021/acs.jctc.0c00228. Epub 2020 May 19. J Chem Theory Comput. 2020. PMID: 32384244

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