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Sandro Bottaro
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Promoting transparency and reproducibility in enhanced molecular simulations
M Bonomi, G Bussi, C Camilloni, GA Tribello, P Banáš, A Barducci, ...
Nature methods 16 (8), 670-673, 2019
6482019
RNA structural dynamics as captured by molecular simulations: A comprehensive overview
J Šponer, G Bussi, M Krepl, P Banáš, S Bottaro, RA Cunha, A Gil-Ley, ...
Chemical reviews 118 (8), 4177-4338, 2018
4322018
Biophysical experiments and biomolecular simulations: A perfect match?
S Bottaro, K Lindorff-Larsen
Science 361 (6400), 355-360, 2018
2442018
The role of nucleobase interactions in RNA structure and dynamics
S Bottaro, F Di Palma, G Bussi
Nucleic acids research 42 (21), 13306-13314, 2014
1302014
Integrating molecular simulation and experimental data: a Bayesian/maximum entropy reweighting approach
S Bottaro, T Bengtsen, K Lindorff-Larsen
Structural Bioinformatics, 219-240, 2020
1272020
Computer folding of RNA tetraloops: identification of key force field deficiencies
P Kührová, RB Best, S Bottaro, G Bussi, J Šponer, M Otyepka, P Banáš
Journal of Chemical Theory and Computation 12 (9), 4534-4548, 2016
1232016
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
S Bottaro, G Bussi, SD Kennedy, DH Turner, K Lindorff-Larsen
Science Advances 4 (5), eaar8521, 2018
1052018
Potentials of mean force for protein structure prediction vindicated, formalized and generalized
T Hamelryck, M Borg, M Paluszewski, J Paulsen, J Frellsen, C Andreetta, ...
PloS one 5 (11), e13714, 2010
1012010
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
AH Larsen, Y Wang, S Bottaro, S Grudinin, L Arleth, K Lindorff-Larsen
PLOS Computational Biology 16 (4), e1007870, 2020
842020
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
S Bottaro, P Banáš, J Sponer, G Bussi
Journal of Physical Chemistry Letters 7 (20), 4032-4038, 2016
802016
How to learn from inconsistencies: Integrating molecular simulations with experimental data
S Orioli, AH Larsen, S Bottaro, K Lindorff-Larsen
Computational Approaches for Understanding Dynamical Systems: Protein …, 2020
732020
Empirical corrections to the amber RNA force field with target metadynamics
A Gil-Ley, S Bottaro, G Bussi
Journal of chemical theory and computation 12 (6), 2790-2798, 2016
652016
Barnaba: software for analysis of nucleic acid structures and trajectories
S Bottaro, G Bussi, G Pinamonti, S Reisser, W Boomsma, ...
RNA 25 (2), 219, 2019
562019
Barnaba: software for analysis of nucleic acid structures and trajectories
S Bottaro, G Bussi, G Pinamonti, S Reißer, W Boomsma, K Lindorff-Larsen
RNA 25 (2), 219-231, 2019
562019
Fitting corrections to an RNA force field using experimental data
A Cesari, S Bottaro, K Lindorff-Larsen, P Banáš, J Šponer, G Bussi
Journal of chemical theory and computation 15 (6), 3425-3431, 2019
512019
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
G Pinamonti, S Bottaro, C Micheletti, G Bussi
Nucleic Acids Research 43 (15), 7260-9, 2015
502015
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
T Bengtsen, VL Holm, LR Kjřlbye, SR Midtgaard, NT Johansen, G Tesei, ...
eLife 9, e56518, 2020
492020
Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data
S Bottaro, K Lindorff-Larsen, RB Best
Journal of chemical theory and computation 9 (12), 5641-5652, 2013
492013
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure
W Boomsma, J Frellsen, T Harder, S Bottaro, KE Johansson, P Tian, ...
Journal of computational chemistry 34 (19), 1697-1705, 2013
482013
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure
W Boomsma, J Frellsen, T Harder, S Bottaro, KE Johansson, P Tian, ...
Journal of computational chemistry 34 (19), 1697-1705, 2013
482013
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