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Items: 9

1.

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models.

Pinamonti G, Paul F, Noé F, Rodriguez A, Bussi G.

J Chem Phys. 2019 Apr 21;150(15):154123. doi: 10.1063/1.5083227.

PMID:
31005065
2.

Barnaba: software for analysis of nucleic acid structures and trajectories.

Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K.

RNA. 2019 Feb;25(2):219-231. doi: 10.1261/rna.067678.118. Epub 2018 Nov 12.

PMID:
30420522
3.

The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family.

Yrazu FM, Pinamonti G, Clementi C.

J Phys Chem B. 2018 Dec 13;122(49):11800-11806. doi: 10.1021/acs.jpcb.8b08676. Epub 2018 Oct 16.

PMID:
30277393
4.

Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex.

Pinamonti G, Campo G, Chen J, Kluber A, Clementi C.

Biophys J. 2018 Oct 16;115(8):1470-1480. doi: 10.1016/j.bpj.2018.08.043. Epub 2018 Sep 7.

PMID:
30268539
5.

Learning Effective Molecular Models from Experimental Observables.

Chen J, Chen J, Pinamonti G, Clementi C.

J Chem Theory Comput. 2018 Jul 10;14(7):3849-3858. doi: 10.1021/acs.jctc.8b00187. Epub 2018 Jun 13.

PMID:
29806937
6.

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.

Chem Rev. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. Epub 2018 Jan 3.

7.

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.

Pinamonti G, Zhao J, Condon DE, Paul F, Noè F, Turner DH, Bussi G.

J Chem Theory Comput. 2017 Feb 14;13(2):926-934. doi: 10.1021/acs.jctc.6b00982. Epub 2017 Jan 5.

8.

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

Pinamonti G, Bottaro S, Micheletti C, Bussi G.

Nucleic Acids Res. 2015 Sep 3;43(15):7260-9. doi: 10.1093/nar/gkv708. Epub 2015 Jul 17.

9.

Stochastic resonance crossovers in complex networks.

Pinamonti G, Marro J, Torres JJ.

PLoS One. 2012;7(12):e51170. doi: 10.1371/journal.pone.0051170. Epub 2012 Dec 14.

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