Bussi G - Search Results

1

Arginine multivalency stabilizes protein/RNA condensates.

Paloni M, Bussi G, Barducci A. Paloni M, et al. Among authors: bussi g. Protein Sci. 2021 Jul;30(7):1418-1426. doi: 10.1002/pro.4109. Epub 2021 May 22. Protein Sci. 2021. PMID: 33982350 Free PMC article.

2

Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

Barducci A, Bussi G, Parrinello M. Barducci A, et al. Among authors: bussi g. Phys Rev Lett. 2008 Jan 18;100(2):020603. doi: 10.1103/PhysRevLett.100.020603. Epub 2008 Jan 18. Phys Rev Lett. 2008. PMID: 18232845

3

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.

4

The role of nucleobase interactions in RNA structure and dynamics.

Bottaro S, Di Palma F, Bussi G. Bottaro S, et al. Among authors: bussi g. Nucleic Acids Res. 2014 Dec 1;42(21):13306-14. doi: 10.1093/nar/gku972. Epub 2014 Oct 29. Nucleic Acids Res. 2014. PMID: 25355509 Free PMC article.

5

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.

Pinamonti G, Bottaro S, Micheletti C, Bussi G. Pinamonti G, et al. Among authors: bussi g. Nucleic Acids Res. 2015 Sep 3;43(15):7260-9. doi: 10.1093/nar/gkv708. Epub 2015 Jul 17. Nucleic Acids Res. 2015. PMID: 26187990 Free PMC article.

6

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Pérez-Villa A, Darvas M, Bussi G. Pérez-Villa A, et al. Among authors: bussi g. Nucleic Acids Res. 2015 Oct 15;43(18):8725-34. doi: 10.1093/nar/gkv872. Epub 2015 Sep 10. Nucleic Acids Res. 2015. PMID: 26358809 Free PMC article.

7

Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.

Gil-Ley A, Bottaro S, Bussi G. Gil-Ley A, et al. Among authors: bussi g. J Chem Theory Comput. 2016 Jun 14;12(6):2790-8. doi: 10.1021/acs.jctc.6b00299. Epub 2016 May 16. J Chem Theory Comput. 2016. PMID: 27153317 Free PMC article.

8

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.

9

Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics.

Poblete S, Bottaro S, Bussi G. Poblete S, et al. Among authors: bussi g. Biochem Biophys Res Commun. 2018 Mar 29;498(2):352-358. doi: 10.1016/j.bbrc.2017.12.057. Epub 2017 Dec 14. Biochem Biophys Res Commun. 2018. PMID: 29248728

10

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. Šponer J, et al. Among authors: bussi g. Chem Rev. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. Epub 2018 Jan 3. Chem Rev. 2018. PMID: 29297679 Free PMC article. Review.

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