Sandro Bottaro

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Citations	3327	2773
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Giovanni BussiScuola Internazionale Superiore di Studi Avanzati, Trieste, ItalyVerified email at sissa.it
Kresten Lindorff-LarsenLinderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenVerified email at bio.ku.dk
Wouter BoomsmaProfessor, Department of Computer Science, University of CopenhagenVerified email at di.ku.dk
Jesper Ferkinghoff-BorgAssociate Professor, Research Director, Novo Nordisk A/SVerified email at novonordisk.com
Thomas HamelryckDpt. of computer science / Dpt. of biology, University of CopenhagenVerified email at bio.ku.dk
Giovanni PinamontiFreie Universität, BerlinVerified email at fu-berlin.de
Alejandro Gil-LeyMetaphore BiotechnologiesVerified email at metaphorebio.com
Simón PobleteAssistant Professor. Universidad San Sebastián, Fundación Ciencia y VidaVerified email at cienciavida.org
Christian AndreettaUniv. of Copenhagen, Denmark, and Uni Computing, Uni Research, NorwayVerified email at uni.no
Jes FrellsenAssociate Professor, Technical University of Denmark (DTU)Verified email at dtu.dk
Francesco Di PalmaIstituto Italiano di TecnologiaVerified email at iit.it
Robert BestSenior Investigator, National Institutes of HealthVerified email at helix.nih.gov
Richard André CunhaUniversity of ZurichVerified email at chem.uzh.ch
Nils G WalterUniversity of Michigan, Ann ArborVerified email at umich.edu
Tone BengtsenPostdoc, machine learning and proteins, Department of Computer Science, University of CopenhagenVerified email at bio.ku.dk
Andreas Haahr LarsenUniversity of CopenhagenVerified email at sund.ku.dk
Simon OlssonChalmers University of TechnologyVerified email at chalmers.se
Tim HarderResearch Scientist at Philips ResearchVerified email at philips.com
Lise ArlethProfessor in Experimental Biophysics, University of CopenhagenVerified email at nbi.ku.dk
Kristoffer Enøe JohanssonDepartment of Biology, University of CopenhagenVerified email at bio.ku.dk

Sandro Bottaro

Peptone

Verified email at peptone.io

RNA modeling Molecular Dynamics Integrative structural biology Computational Biology


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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	778	2019
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	490	2018
Biophysical experiments and biomolecular simulations: A perfect match? S Bottaro, K Lindorff-Larsen Science 361 (6400), 355-360, 2018	263	2018
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	146	2014
Integrating molecular simulation and experimental data: a Bayesian/maximum entropy reweighting approach S Bottaro, T Bengtsen, K Lindorff-Larsen Structural Bioinformatics, 219-240, 2020	139	2020
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	130	2016
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	117	2018
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	102	2010
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	92	2020
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	87	2016
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	77	2020
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	67	2019
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	67	2019
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	67	2016
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	57	2019
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations T Bengtsen, VL Holm, LR Kjølbye, SR Midtgaard, NT Johansen, G Tesei, ... eLife 9, e56518, 2020	53	2020
Mapping the universe of RNA tetraloop folds S Bottaro, K Lindorff-Larsen Biophysical journal 113 (2), 257-267, 2017	50	2017
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	50	2015
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	49	2013
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	48	2013

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