BOTTARO, SANDRO
BOTTARO, SANDRO
Dipartimento Scienze Biomediche
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
2018-01-01 Poblete Fuentes, Simon David; Bottaro, Sandro; Bussi, Giovanni
Accuracy of the pseudopotential approximation in ab initio theoretical spectroscopies
2008-01-01 Luppi, E; Weissker, H; Bottaro, S; Sottile, F; Veniard, V; Reining, L; Onida, G
Accurate multiple time step in biased molecular simulations
2015-01-01 Ferrarotti, M. J.; Bottaro, Sandro; Perez Villa, Andrea; Bussi, Giovanni
An Efficient Null Model for Conformational Fluctuations in Proteins
2012-01-01 Harder, T; Borg, M; Bottaro, S; Boomsma, W; Olsson, S; Ferkinghoff-Borg, J; Hamelryck, T
Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages
2018-01-01 Cesari, Andrea; Bottaro, Sandro; Bussi, Giovanni
Barnaba: software for analysis of nucleic acid structures and trajectories
2019-01-01 Bottaro, Sandro; Bussi, Giovanni; Pinamonti, Giovanni; Reißer, Sabine; Boomsma, Wouter; Lindorff-Larsen, Kresten
Biophysical experiments and biomolecular simulations: A perfect match?
2018-01-01 Bottaro, S; Lindorff-Larsen, K
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
2020-01-01 Larsen, Ah; Wang, Y; Bottaro, S; Grudinin, S; Arleth, L; Lindorff-Larsen, K
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
2016-01-01 Kührová, P.; Best, R. B.; Bottaro, Sandro; Bussi, Giovanni; Šponer, J.; Otyepka, M.; Banáš, P.
Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations
2021-01-01 Bottaro, Sandro; Bussi, Giovanni; Lindorff-Larsen, Kresten
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
2018-01-01 Bottaro, Sandro; Bussi, Giovanni; Kennedy, Scott D.; Turner, Douglas H.; Lindorff-Larsen, Kresten
Conformational Heterogeneity of UCAAUC RNA Oligonucleotide from Molecular Dynamics Simulations, SAXS, and NMR experiments
2022-01-01 Bergonzo, Christina; Grishaev, Alexander V; Bottaro, Sandro
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics
2018-01-01 Poblete, Simón; Bottaro, S; Bussi, Giovanni
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
2015-01-01 Pinamonti, G.; Bottaro, S.; Micheletti, C.; Bussi, G.
Empirical corrections to the Amber RNA force field with Target Metadynamics
2016-01-01 Gil Ley, Alejandro; Bottaro, Sandro; Bussi, Giovanni
Fitting Corrections to an RNA Force Field Using Experimental Data
2019-01-01 Cesari, A; Bottaro, S; Lindorfr-Larsen, K; Banas, P; Sponer, J; Bussi, G
Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method
2014-01-01 Valentin, B.; Andreetta, C; Boomsma, W; Bottaro, S; Ferkinghoff-Borg, J; Frellsen, J; Mardia, K.; Tian, P; Hamelryck, T
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
2016-01-01 Bottaro, Sandro; Banáš, P.; Šponer, J.; Bussi, Giovanni
Generative probabilistic models extend the scope of inferential structure determination
2011-01-01 Olsson, S; Boomsma, W; Frellsen, J; Bottaro, S; Harder, T; Ferkinghoff-Borg, J; Hamelryck, T
How to learn from inconsistencies: Integrating molecular simulations with experimental data
2020-01-01 Orioli, S; Larsen, Ah; Bottaro, S; Lindorff-Larsen, K