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Items: 38

1.

Fitting Corrections to an RNA Force Field Using Experimental Data.

Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Šponer J, Bussi G.

J Chem Theory Comput. 2019 Jun 11;15(6):3425-3431. doi: 10.1021/acs.jctc.9b00206. Epub 2019 May 23.

PMID:
31050905
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.

Biophysical experiments and biomolecular simulations: A perfect match?

Bottaro S, Lindorff-Larsen K.

Science. 2018 Jul 27;361(6400):355-360. doi: 10.1126/science.aat4010. Review.

PMID:
30049874
4.

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

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K.

Sci Adv. 2018 May 18;4(5):eaar8521. doi: 10.1126/sciadv.aar8521. eCollection 2018 May.

5.

Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops".

Bottaro S, Banáš P, Šponer J, Bussi G.

J Phys Chem Lett. 2018 Apr 5;9(7):1674-1675. doi: 10.1021/acs.jpclett.8b00754. Epub 2018 Mar 19. No abstract available.

PMID:
29553740
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.

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

Poblete S, Bottaro S, Bussi G.

Nucleic Acids Res. 2018 Feb 28;46(4):1674-1683. doi: 10.1093/nar/gkx1269.

8.

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

Poblete S, Bottaro S, 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.

PMID:
29248728
9.

Mapping the Universe of RNA Tetraloop Folds.

Bottaro S, Lindorff-Larsen K.

Biophys J. 2017 Jul 25;113(2):257-267. doi: 10.1016/j.bpj.2017.06.011. Epub 2017 Jun 30.

10.

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.

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

11.

Free Energy Landscape of GAGA and UUCG RNA Tetraloops.

Bottaro S, Banáš P, Šponer J, Bussi G.

J Phys Chem Lett. 2016 Oct 20;7(20):4032-4038. Epub 2016 Sep 28. Erratum in: J Phys Chem Lett. 2018 Apr 5;9(7):1674-1675.

PMID:
27661094
12.

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.

J Chem Theory Comput. 2016 Sep 13;12(9):4534-48. doi: 10.1021/acs.jctc.6b00300. Epub 2016 Aug 4.

13.

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

Gil-Ley A, Bottaro S, Bussi G.

J Chem Theory Comput. 2016 Jun 14;12(6):2790-8. doi: 10.1021/acs.jctc.6b00299. Epub 2016 May 16.

14.

RNA folding pathways in stop motion.

Bottaro S, Gil-Ley A, Bussi G.

Nucleic Acids Res. 2016 Jul 8;44(12):5883-91. doi: 10.1093/nar/gkw239. Epub 2016 Apr 18.

15.

European Network for Patient Safety and Quality of Care: PaSQ.

Bottaro S, Garel P, Agra Y.

Rev Calid Asist. 2016 Jun;31 Suppl 1:1-3. doi: 10.1016/j.cali.2015.12.010. Epub 2016 Mar 3. No abstract available.

PMID:
26946969
16.

Accurate multiple time step in biased molecular simulations.

Ferrarotti MJ, Bottaro S, Pérez-Villa A, Bussi G.

J Chem Theory Comput. 2015 Jan 13;11(1):139-46. doi: 10.1021/ct5007086. Epub 2014 Dec 23.

PMID:
26574212
17.

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.

18.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

Di Palma F, Bottaro S, Bussi G.

BMC Bioinformatics. 2015;16 Suppl 9:S6. doi: 10.1186/1471-2105-16-S9-S6. Epub 2015 Jun 1.

19.

Passive transfer of affinity-purified anti-heart autoantibodies (AHA) from sera of patients with myocarditis induces experimental myocarditis in mice.

Caforio AL, Angelini A, Blank M, Shani A, Kivity S, Goddard G, Doria A, Schiavo A, Testolina M, Bottaro S, Marcolongo R, Thiene G, Iliceto S, Shoenfeld Y.

Int J Cardiol. 2015 Jan 20;179:166-77. doi: 10.1016/j.ijcard.2014.10.165. Epub 2014 Oct 29.

PMID:
25464438
20.

The role of nucleobase interactions in RNA structure and dynamics.

Bottaro S, Di Palma F, Bussi G.

Nucleic Acids Res. 2014 Dec 1;42(21):13306-14. doi: 10.1093/nar/gku972. Epub 2014 Oct 29.

21.
22.

Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.

Valentin JB, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J, Frellsen J, Mardia KV, Tian P, Hamelryck T.

Proteins. 2014 Feb;82(2):288-99. doi: 10.1002/prot.24386. Epub 2013 Oct 17.

PMID:
23934827
23.

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.

J Comput Chem. 2013 Jul 15;34(19):1697-705. doi: 10.1002/jcc.23292. Epub 2013 Apr 26.

PMID:
23619610
24.

An efficient null model for conformational fluctuations in proteins.

Harder T, Borg M, Bottaro S, Boomsma W, Olsson S, Ferkinghoff-Borg J, Hamelryck T.

Structure. 2012 Jun 6;20(6):1028-39. doi: 10.1016/j.str.2012.03.020. Epub 2012 May 10.

25.

Subtle Monte Carlo Updates in Dense Molecular Systems.

Bottaro S, Boomsma W, E Johansson K, Andreetta C, Hamelryck T, Ferkinghoff-Borg J.

J Chem Theory Comput. 2012 Feb 14;8(2):695-702. doi: 10.1021/ct200641m. Epub 2012 Jan 18.

PMID:
26596617
26.

Generative probabilistic models extend the scope of inferential structure determination.

Olsson S, Boomsma W, Frellsen J, Bottaro S, Harder T, Ferkinghoff-Borg J, Hamelryck T.

J Magn Reson. 2011 Dec;213(1):182-6. doi: 10.1016/j.jmr.2011.08.039. Epub 2011 Sep 6.

PMID:
21993764
27.

Potentials of mean force for protein structure prediction vindicated, formalized and generalized.

Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J.

PLoS One. 2010 Nov 10;5(11):e13714. doi: 10.1371/journal.pone.0013714.

28.

Anti-heart and anti-intercalated disk autoantibodies: evidence for autoimmunity in idiopathic recurrent acute pericarditis.

Caforio AL, Brucato A, Doria A, Brambilla G, Angelini A, Ghirardello A, Bottaro S, Tona F, Betterle C, Daliento L, Thiene G, Iliceto S.

Heart. 2010 May;96(10):779-84. doi: 10.1136/hrt.2009.187138.

29.

Effectiveness of an intervention to improve breastfeeding knowledge and attitudes among fifth-grade children in Brazil.

Bottaro SM, Giugliani ER.

J Hum Lact. 2009 Aug;25(3):325-32. doi: 10.1177/0890334409337248. Epub 2009 Jun 1.

PMID:
19487704
30.

[Exploratory survey of fifth-grade elementary students in relation to breastfeeding].

Bottaro SM, Giugliani ER.

Cad Saude Publica. 2008 Jul;24(7):1599-608. Portuguese.

31.

Clinical implications of anti-heart autoantibodies in myocarditis and dilated cardiomyopathy.

Caforio AL, Tona F, Bottaro S, Vinci A, Dequal G, Daliento L, Thiene G, Iliceto S.

Autoimmunity. 2008 Feb;41(1):35-45. doi: 10.1080/08916930701619235. Review.

PMID:
18176863
32.

A prospective study of biopsy-proven myocarditis: prognostic relevance of clinical and aetiopathogenetic features at diagnosis.

Caforio AL, Calabrese F, Angelini A, Tona F, Vinci A, Bottaro S, Ramondo A, Carturan E, Iliceto S, Thiene G, Daliento L.

Eur Heart J. 2007 Jun;28(11):1326-33. Epub 2007 May 9.

PMID:
17493945
33.

Autoimmune myocarditis and dilated cardiomyopathy: focus on cardiac autoantibodies.

Caforio AL, Daliento L, Angelini A, Bottaro S, Vinci A, Dequal G, Tona F, Iliceto S, Thiene G, McKenna WJ.

Lupus. 2005;14(9):652-5. Review.

PMID:
16218460
34.

Acute effects of the oral administration of midodrine, an alpha-adrenergic agonist, on renal hemodynamics and renal function in cirrhotic patients with ascites.

Angeli P, Volpin R, Piovan D, Bortoluzzi A, Craighero R, Bottaro S, Finucci GF, Casiglia E, Sticca A, De Toni R, Pavan L, Gatta A.

Hepatology. 1998 Oct;28(4):937-43.

PMID:
9755229
35.

Pharmaceutical services in the United States Army.

Williams RF, Moran EL, Bottaro SD 2nd, Dydek GJ, Caouette ML, Thomas JD, Echevarria R.

Am J Health Syst Pharm. 1997 Apr 1;54(7):773-8.

PMID:
9099343
36.

Determination of inulin in plasma and urine by reversed-phase high-performance liquid chromatography.

Dall'Amico R, Montini G, Pisanello L, Piovesan G, Bottaro S, Cracco AT, Zacchello G, Zacchello F.

J Chromatogr B Biomed Appl. 1995 Oct 6;672(1):155-9.

PMID:
8590929
37.

Determination of 8-methoxypsoralen in plasma by gas chromatography-mass spectrometry using selected-ion monitoring.

Cracco AT, Dall'Amico R, Ferrari V, Bottaro S, Zacchello G, Chiandetti L, Zacchello F.

J Chromatogr. 1992 Feb 7;574(1):156-60.

PMID:
1629281
38.

A new design for an exploring chemode.

Bronzino JD, Morgane PJ, Stern WC, Bottaro S.

Electroencephalogr Clin Neurophysiol. 1972 Feb;32(2):195-8. No abstract available.

PMID:
4109347

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