Bottaro S - Search Results

1

Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop.

Oxenfarth A, Kümmerer F, Bottaro S, Schnieders R, Pinter G, Jonker HRA, Fürtig B, Richter C, Blackledge M, Lindorff-Larsen K, Schwalbe H. Oxenfarth A, et al. Among authors: bottaro s. J Am Chem Soc. 2023 Aug 2;145(30):16557-16572. doi: 10.1021/jacs.3c03578. Epub 2023 Jul 21. J Am Chem Soc. 2023. PMID: 37479220 Free PMC article.

2

Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations.

Bottaro S, Bussi G, Lindorff-Larsen K. Bottaro S, et al. J Am Chem Soc. 2021 Jun 9;143(22):8333-8343. doi: 10.1021/jacs.1c01094. Epub 2021 May 26. J Am Chem Soc. 2021. PMID: 34039006

3

Mapping the Universe of RNA Tetraloop Folds.

Bottaro S, Lindorff-Larsen K. Bottaro S, et al. Biophys J. 2017 Jul 25;113(2):257-267. doi: 10.1016/j.bpj.2017.06.011. Epub 2017 Jun 30. Biophys J. 2017. PMID: 28673616 Free PMC article.

4

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Bottaro S, et al. Sci Adv. 2018 May 18;4(5):eaar8521. doi: 10.1126/sciadv.aar8521. eCollection 2018 May. Sci Adv. 2018. PMID: 29795785 Free PMC article.

5

Biophysical experiments and biomolecular simulations: A perfect match?

Bottaro S, Lindorff-Larsen K. Bottaro S, et al. Science. 2018 Jul 27;361(6400):355-360. doi: 10.1126/science.aat4010. Science. 2018. PMID: 30049874 Review.

6

Fitting Corrections to an RNA Force Field Using Experimental Data.

Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Šponer J, Bussi G. Cesari A, et al. Among authors: bottaro s. J Chem Theory Comput. 2019 Jun 11;15(6):3425-3431. doi: 10.1021/acs.jctc.9b00206. Epub 2019 May 23. J Chem Theory Comput. 2019. PMID: 31050905

7

Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach.

Bottaro S, Bengtsen T, Lindorff-Larsen K. Bottaro S, et al. Methods Mol Biol. 2020;2112:219-240. doi: 10.1007/978-1-0716-0270-6_15. Methods Mol Biol. 2020. PMID: 32006288

8

Integrating NMR and simulations reveals motions in the UUCG tetraloop.

Bottaro S, Nichols PJ, Vögeli B, Parrinello M, Lindorff-Larsen K. Bottaro S, et al. Nucleic Acids Res. 2020 Jun 19;48(11):5839-5848. doi: 10.1093/nar/gkaa399. Nucleic Acids Res. 2020. PMID: 32427326 Free PMC article.

9

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.

Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Larsen AH, et al. Among authors: bottaro s. PLoS Comput Biol. 2020 Apr 27;16(4):e1007870. doi: 10.1371/journal.pcbi.1007870. eCollection 2020 Apr. PLoS Comput Biol. 2020. PMID: 32339173 Free PMC article.

10

Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

Bottaro S, Lindorff-Larsen K, Best RB. Bottaro S, et al. J Chem Theory Comput. 2013 Dec 10;9(12):5641-5652. doi: 10.1021/ct400730n. J Chem Theory Comput. 2013. PMID: 24748852 Free PMC article.

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