Bottaro S - Search Results

1

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.

2

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.

Boomsma W, Frellsen J, Harder T, Bottaro S, Johansson KE, Tian P, Stovgaard K, Andreetta C, Olsson S, Valentin JB, Antonov LD, Christensen AS, Borg M, Jensen JH, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T. Boomsma W, et al. Among authors: bottaro s. J Comput Chem. 2013 Jul 15;34(19):1697-705. doi: 10.1002/jcc.23292. Epub 2013 Apr 26. J Comput Chem. 2013. PMID: 23619610

3

Accurate multiple time step in biased molecular simulations.

Ferrarotti MJ, Bottaro S, Pérez-Villa A, Bussi G. Ferrarotti MJ, et al. Among authors: bottaro s. 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

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: bottaro s. 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.

5

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: bottaro s. 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.

6

Correction to 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. 2017 Jan 10;13(1):392. doi: 10.1021/acs.jctc.6b01188. Epub 2016 Dec 19. J Chem Theory Comput. 2017. PMID: 27990814 Free PMC article. No abstract available.

7

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.

8

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.

9

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.

10

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

Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K. Bottaro S, et al. RNA. 2019 Feb;25(2):219-231. doi: 10.1261/rna.067678.118. Epub 2018 Nov 12. RNA. 2019. PMID: 30420522 Free PMC article.

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