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)

Structural alphabets derived from attractors in conformational space. - Alessandro Pandini; Arianna Fornili; Jens Kleinjung (BMC Bioinform., 2010)

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)

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. - Alessandro Pandini; Arianna Fornili; Franca Fraternali; Jens Kleinjung (Bioinform., 2013)

Deep Autoencoders for Additional Insight into Protein Dynamics. - Mihai Teletin; Gabriela Czibula; Maria-Iuliana Bocicor; Silvana Iuliana Albert; Alessandro Pandini (ICANN (2), 2018)

In silico identification of rescue sites by double force scanning. - Matteo Tiberti; Alessandro Pandini; Franca Fraternali; Arianna Fornili (Bioinform., 2018)

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

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II. - Alessandro Pandini; Howard Schulman; Shahid Khan 005 (PLoS Comput. Biol., 2019)

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites. - Eunice Cho; Margarida Rosa; Ruhi Anjum; Saman Mehmood; Mariya Soban; Moniza Mujtaba; Khair Bux; Syed Tarique Moin; Mohammad Tanweer; Sarath Dantu; Alessandro Pandini; Junqi Yin; et al. (J. Chem. Inf. Model., 2021)

MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams. - Boris Gomaz; Alessandro Pandini; Aleksandra Marsavelski; Zoran Stefanic (J. Chem. Inf. Model., 2024)