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Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations 1-gen-2018 Bottaro, Sandro; Bussi, Giovanni; Kennedy, Scott D.; Turner, Douglas H.; Lindorff-Larsen, Kresten
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs 1-gen-2018 Poblete Fuentes, Simon David; Bottaro, Sandro; Bussi, Giovanni
Biophysical experiments and biomolecular simulations: A perfect match? 1-gen-2018 Bottaro, S; Lindorff-Larsen, K
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview 1-gen-2018 Šponer, Jiří; Bussi, Giovanni; Krepl, Miroslav; Banáš, Pavel; Bottaro, Sandro; Cunha, Richard A; Gil-Ley, Alejandro; Pinamonti, Giovanni; Poblete, Simón; Jurečka, Petr; Walter, Nils G; Otyepka, Michal
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics 1-gen-2018 Poblete, Simón; Bottaro, S; Bussi, Giovanni
Promoting transparency and reproducibility in enhanced molecular simulations 1-gen-2019 Bonomi, M; Bussi, G; Camilloni, C; Tribello, Ga; Banas, P; Barducci, A; Bernetti, M; Bolhuis, Pg; Bottaro, S; Branduardi, D; Capelli, R; Carloni, P; Ceriotti, M; Cesari, A; Chen, Hc; Chen, W; Colizzi, F; De, S; De La Pierre, M; Donadio, D; Drobot, V; Ensing, B; Ferguson, Al; Filizola, M; Fraser, Js; Fu, Hh; Gasparotto, P; Gervasio, Fl; Giberti, F; Gil-Ley, A; Giorgino, T; Heller, Gt; Hocky, Gm; Iannuzzi, M; Invernizzi, M; Jelfs, Ke; Jussupow, A; Kirilin, E; Laio, A; Limongelli, V; Lindorff-Larsen, K; Lohr, T; Marinelli, F; Martin-Samos, L; Masetti, M; Meyer, R; Michaelides, A; Molteni, C; Morishita, T; Nava, M; Paissoni, C; Papaleo, E; Parrinello, M; Pfaendtner, J; Piaggi, P; Piccini, G; Pietropaolo, A; Pietrucci, F; Pipolo, S; Provasi, D; Quigley, D; Raiteri, P; Raniolo, S; Rydzewski, J; Salvalaglio, M; Sosso, Gc; Spiwok, V; Sponer, J; Swenson, Dwh; Tiwary, P; Valsson, O; Vendruscolo, M; Voth, Ga; White, A
Fitting Corrections to an RNA Force Field Using Experimental Data 1-gen-2019 Cesari, A; Bottaro, S; Lindorfr-Larsen, K; Banas, P; Sponer, J; Bussi, G
Barnaba: software for analysis of nucleic acid structures and trajectories 1-gen-2019 Bottaro, Sandro; Bussi, Giovanni; Pinamonti, Giovanni; Reißer, Sabine; Boomsma, Wouter; Lindorff-Larsen, Kresten
How to learn from inconsistencies: Integrating molecular simulations with experimental data 1-gen-2020 Orioli, S; Larsen, Ah; Bottaro, S; Lindorff-Larsen, K
Integrating molecular simulation and experimental data: a Bayesian/maximum entropy reweighting approach 1-gen-2020 Bottaro, S; Bengtsen, T; Kresten Lindorff-Larsen, K
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution 1-gen-2020 Larsen, Ah; Wang, Y; Bottaro, S; Grudinin, S; Arleth, L; Lindorff-Larsen, K
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations 1-gen-2020 Bengtsen, T; Holm, V L; Lisbeth Ravnkilde, Kjølbye; Søren, R Midtgaard; Nicolai Tidemand, Johansen; Giulio, Tesei; Bottaro, S; Birgit, Schiøtt; Lise, Arleth; Kresten, Lindorff-Larsen
Integrating NMR and simulations reveals motions in the UUCG tetraloop 1-gen-2020 Bottaro, S; Nichols, Pj; Vögeli, B; Parrinello, M; Lindorff-Larsen, K
Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations 1-gen-2021 Bottaro, Sandro; Bussi, Giovanni; Lindorff-Larsen, Kresten
MEDTEC Students against Coronavirus: Investigating the Role of Hemostatic Genes in the Predisposition to COVID-19 Severity 1-gen-2021 Cappadona, Claudio; Paraboschi, Elvezia Maria; Ziliotto, Nicole; Bottaro, Sandro; Rimoldi, Valeria; Gerussi, Alessio; Azimonti, Andrea; Brenna, Daniele; Brunati, Andrea; Cameroni, Charlotte; Campanaro, Giovanni; Carloni, Francesca; Cavadini, Giacomo; Ciravegna, Martina; Composto, Antonio; Converso, Giuseppe; Corbella, Pierluigi; D'Eugenio, Davide; Dal Rì, Giovanna; Di Giorgio, Sofia Maria; Grondelli, Maria Chiara; Guerrera, Lorenza; Laffoucriere, Georges; Lando, Beatrice; Lopedote, Leandro; Maizza, Benedetta; Marconi, Elettra; Mariola, Carlotta; Matronola, Guia Margherita; Menga, Luca Maria; Montorsi, Giulia; Papatolo, Antonio; Patti, Riccardo; Profeta, Lorenzo; Rebasti, Vera; Smidili, Alice; Tarchi, Sofia Maria; Tartaglia, Francesco Carlo; Tettamanzi, Gaia; Tinelli, Elena; Stuani, Riccardo; Bolchini, Cristiana; Pattini, Linda; Invernizzi, Pietro; Degenhardt, Frauke; Franke, Andre; Duga, Stefano; Asselta, Rosanna
LLM-PBC: Logic Learning Machine-Based Explainable Rules Accurately Stratify the Genetic Risk of Primary Biliary Cholangitis 1-gen-2022 Gerussi, Alessio; Verda, Damiano; Cappadona, Claudio; Cristoferi, Laura; Bernasconi, Davide Paolo; Bottaro, Sandro; Carbone, Marco; Muselli, Marco; Invernizzi, Pietro; Asselta, Rosanna; On Behalf Of The Italian Pbc Genetics Study Group, Null
Conformational Heterogeneity of UCAAUC RNA Oligonucleotide from Molecular Dynamics Simulations, SAXS, and NMR experiments 1-gen-2022 Bergonzo, Christina; Grishaev, Alexander V; Bottaro, Sandro
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