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Sandro Bottaro - Publications

Affiliations: 
Italian Institute of Technology, Genoa, United States 
Area:
Molecular Dynamics; Biophysics; Computational chemistry
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Oxenfarth A, Kümmerer F, Bottaro S, Schnieders R, Pinter G, Jonker HRA, Fürtig B, Richter C, Blackledge M, Lindorff-Larsen K, Schwalbe H. Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop. Journal of the American Chemical Society. PMID 37479220 DOI: 10.1021/jacs.3c03578  0.652
2023 Cagiada M, Bottaro S, Lindemose S, Schenstrøm SM, Stein A, Hartmann-Petersen R, Lindorff-Larsen K. Discovering functionally important sites in proteins. Nature Communications. 14: 4175. PMID 37443362 DOI: 10.1038/s41467-023-39909-0  0.479
2022 Bergonzo C, Grishaev AV, Bottaro S. Conformational Heterogeneity of UCAAUC RNA Oligonucleotide from Molecular Dynamics Simulations, SAXS, and NMR experiments. Rna (New York, N.Y.). PMID 35483823 DOI: 10.1261/rna.078888.121  0.521
2021 Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. Journal of the American Chemical Society. 143: 8333-8343. PMID 34039006 DOI: 10.1021/jacs.1c01094  0.831
2020 Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K. Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations. Elife. 9. PMID 32729831 DOI: 10.7554/Elife.56518  0.71
2020 Bottaro S, Nichols PJ, Vögeli B, Parrinello M, Lindorff-Larsen K. Integrating NMR and simulations reveals motions in the UUCG tetraloop. Nucleic Acids Research. PMID 32427326 DOI: 10.1093/Nar/Gkaa399  0.816
2020 Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. Plos Computational Biology. 16: e1007870. PMID 32339173 DOI: 10.1371/Journal.Pcbi.1007870  0.696
2020 Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. Progress in Molecular Biology and Translational Science. 170: 123-176. PMID 32145944 DOI: 10.1016/Bs.Pmbts.2019.12.006  0.723
2020 Bottaro S, Bengtsen T, Lindorff-Larsen K. Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach. Methods in Molecular Biology (Clifton, N.J.). 2112: 219-240. PMID 32006288 DOI: 10.1007/978-1-0716-0270-6_15  0.74
2020 Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K. Author response: Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations Elife. DOI: 10.7554/Elife.56518.Sa2  0.638
2019 Bonomi M, Bussi G, Camilloni C, Tribello GA, Banáš P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen H, et al. Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods. 16: 670-673. PMID 31363226 DOI: 10.1038/S41592-019-0506-8  0.747
2019 Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Sponer J, Bussi G. Fitting corrections to an RNA force field using experimental data. Journal of Chemical Theory and Computation. PMID 31050905 DOI: 10.1021/Acs.Jctc.9B00206  0.807
2018 Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K. Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories. Rna (New York, N.Y.). PMID 30420522 DOI: 10.1261/Rna.067678.118  0.811
2018 Bottaro S, Lindorff-Larsen K. Biophysical experiments and biomolecular simulations: A perfect match? Science (New York, N.Y.). 361: 355-360. PMID 30049874 DOI: 10.1126/Science.Aat4010  0.711
2018 Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Science Advances. 4: eaar8521. PMID 29795785 DOI: 10.1126/Sciadv.Aar8521  0.84
2018 Bottaro S, Banáš P, Šponer J, Bussi G. Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops". The Journal of Physical Chemistry Letters. 1674-1675. PMID 29553740 DOI: 10.1021/Acs.Jpclett.8B00754  0.742
2018 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. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews. PMID 29297679 DOI: 10.1021/Acs.Chemrev.7B00427  0.806
2018 Cesari A, Bottaro S, Bussi G. Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages Biophysical Journal. 114: 437a. DOI: 10.1016/J.Bpj.2017.11.2417  0.71
2017 Poblete S, Bottaro S, Bussi G. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. Nucleic Acids Research. PMID 29272539 DOI: 10.1093/Nar/Gkx1269  0.758
2017 Poblete S, Bottaro S, Bussi G. Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics. Biochemical and Biophysical Research Communications. PMID 29248728 DOI: 10.1016/J.Bbrc.2017.12.057  0.781
2017 Bottaro S, Lindorff-Larsen K. Mapping the Universe of RNA Tetraloop Folds. Biophysical Journal. 113: 257-267. PMID 28673616 DOI: 10.1016/J.Bpj.2017.06.011  0.684
2017 Bottaro S, Lindorff-Larsen K, Best RB. Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data. Journal of Chemical Theory and Computation. 13: 392. PMID 27990814 DOI: 10.1021/Acs.Jctc.6B01188  0.679
2016 Bottaro S, Banáš P, Šponer J, Bussi G. Free Energy Landscape of GAGA and UUCG RNA Tetraloops. The Journal of Physical Chemistry Letters. 7: 4032-4038. PMID 27661094 DOI: 10.1021/Acs.Jpclett.6B01905  0.776
2016 Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. Journal of Chemical Theory and Computation. 12: 4534-48. PMID 27438572 DOI: 10.1021/Acs.Jctc.6B00300  0.791
2016 Gil-Ley A, Bottaro S, Bussi G. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics. Journal of Chemical Theory and Computation. 12: 2790-8. PMID 27153317 DOI: 10.1021/Acs.Jctc.6B00299  0.814
2016 Bottaro S, Gil-Ley A, Bussi G. RNA folding pathways in stop motion. Nucleic Acids Research. 44: 5883-91. PMID 27091499 DOI: 10.1093/Nar/Gkw239  0.797
2016 Gil-Ley A, Bottaro S, Bussi G. RNA Conformational Ensembles: Narrowing the GAP between Experiments and Simulations with Metadynamics Biophysical Journal. 110: 522a-523a. DOI: 10.1016/J.Bpj.2015.11.2796  0.81
2016 Pinamonti G, Bottaro S, Micheletti C, Bussi G. RNA Conformational Fluctuations from Elastic Network Models: A Comparison with Molecular Dynamics and Shape Experiments Biophysical Journal. 110: 330a. DOI: 10.1016/J.Bpj.2015.11.1772  0.805
2015 Ferrarotti MJ, Bottaro S, Pérez-Villa A, Bussi G. Accurate multiple time step in biased molecular simulations. Journal of Chemical Theory and Computation. 11: 139-46. PMID 26574212 DOI: 10.1021/Ct5007086  0.767
2015 Pinamonti G, Bottaro S, Micheletti C, Bussi G. Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments. Nucleic Acids Research. 43: 7260-9. PMID 26187990 DOI: 10.1093/Nar/Gkv708  0.8
2015 Di Palma F, Bottaro S, Bussi G. Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. Bmc Bioinformatics. 16: S6. PMID 26051557 DOI: 10.1186/1471-2105-16-S9-S6  0.775
2015 Poblete S, Bottaro S, Bussi G. A Nucleobase-Centric Coarse-Grained Model for Structure Prediction of RNA Fragments Biophysical Journal. 108: 235a. DOI: 10.1016/J.Bpj.2014.11.1300  0.796
2014 Bottaro S, Di Palma F, Bussi G. The role of nucleobase interactions in RNA structure and dynamics. Nucleic Acids Research. 42: 13306-14. PMID 25355509 DOI: 10.1093/Nar/Gku972  0.784
2014 Valentin JB, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J, Frellsen J, Mardia KV, Tian P, Hamelryck T. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method. Proteins. 82: 288-99. PMID 23934827 DOI: 10.1002/Prot.24386  0.369
2013 Bottaro S, Lindorff-Larsen K, Best RB. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data. Journal of Chemical Theory and Computation. 9: 5641-5652. PMID 24748852 DOI: 10.1021/Ct400730N  0.708
2013 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, et al. PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure. Journal of Computational Chemistry. 34: 1697-705. PMID 23619610 DOI: 10.1002/Jcc.23292  0.711
2012 Bottaro S, Boomsma W, E Johansson K, Andreetta C, Hamelryck T, Ferkinghoff-Borg J. Subtle Monte Carlo Updates in Dense Molecular Systems. Journal of Chemical Theory and Computation. 8: 695-702. PMID 26596617 DOI: 10.1021/Ct200641M  0.504
2012 Harder T, Borg M, Bottaro S, Boomsma W, Olsson S, Ferkinghoff-Borg J, Hamelryck T. An efficient null model for conformational fluctuations in proteins. Structure (London, England : 1993). 20: 1028-39. PMID 22578545 DOI: 10.1016/J.Str.2012.03.020  0.434
2011 Olsson S, Boomsma W, Frellsen J, Bottaro S, Harder T, Ferkinghoff-Borg J, Hamelryck T. Generative probabilistic models extend the scope of inferential structure determination. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 213: 182-6. PMID 21993764 DOI: 10.1016/J.Jmr.2011.08.039  0.384
2010 Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J. Potentials of mean force for protein structure prediction vindicated, formalized and generalized. Plos One. 5: e13714. PMID 21103041 DOI: 10.1371/Journal.Pone.0013714  0.413
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