MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database. - Alessandro Pandini; Laura Bonati; Franca Fraternali; Jens Kleinjung (Bioinform., 2007)

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps. - Domenico Fraccalvieri; Alessandro Pandini; Fabio Stella; Laura Bonati (BMC Bioinform., 2011)

Predicting the accuracy of protein-ligand docking on homology models. - Annalisa Bordogna; Alessandro Pandini; Laura Bonati (J. Comput. Chem., 2011)

New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability. - Ilaria Motto; Annalisa Bordogna; Anatoly A. Soshilov; Michael S. Denison; Laura Bonati (J. Chem. Inf. Model., 2011)

Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles. - Domenico Fraccalvieri; Laura Bonati; Fabio Stella (WIVACE, 2013)

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR: ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation. - Dario Corrada; Anatoly A. Soshilov; Michael S. Denison; Laura Bonati (PLoS Comput. Biol., 2016)

Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches. - Stefano Motta; Laura Bonati (J. Chem. Inf. Model., 2017)

Ligand-induced perturbation of the HIF-2α: ARNT dimer dynamics. - Stefano Motta; Claudia Minici; Dario Corrada; Laura Bonati; Alessandro Pandini (PLoS Comput. Biol., 2018)

Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations. - Bharath Raghavan; Mirko Paulikat; Katya Ahmad; Lara Callea; Andrea Rizzi; Emiliano Ippoliti; Davide Mandelli; Laura Bonati; Marco de Vivo; Paolo Carloni (J. Chem. Inf. Model., 2023)