Sandro Bottaro
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Ano
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
1852018
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
1222019
Biophysical experiments and biomolecular simulations: A perfect match?
S Bottaro, K Lindorff-Larsen
Science 361 (6400), 355-360, 2018
1012018
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
842014
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
812010
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
692016
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
612018
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
562016
Integrating molecular simulation and experimental data: a Bayesian/maximum entropy reweighting approach
S Bottaro, T Bengtsen, K Lindorff-Larsen
Structural Bioinformatics, 219-240, 2020
422020
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
422016
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
362013
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
362013
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
352015
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
342013
RNA Folding Pathways in Stop-Motion
S Bottaro, A Gil-Ley, G Bussi
Nucleic Acids Research, 2016
312016
Accuracy of the pseudopotential approximation in ab initio theoretical spectroscopies
E Luppi, HC Weissker, S Bottaro, F Sottile, V Veniard, L Reining, G Onida
Physical Review B 78 (24), 245124, 2008
292008
Subtle Monte Carlo updates in dense molecular systems
S Bottaro, W Boomsma, K E. Johansson, C Andreetta, T Hamelryck, ...
Journal of chemical theory and computation 8 (2), 695-702, 2012
282012
Mapping the universe of RNA tetraloop folds
S Bottaro, K Lindorff-Larsen
Biophysical journal 113 (2), 257-267, 2017
272017
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
F Di Palma, S Bottaro, G Bussi
BMC bioinformatics 16 (9), 1-9, 2015
262015
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
242020
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