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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