AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. - Giovanni Bottegoni; Walter Rocchia; Maurizio Recanatini; Andrea Cavalli (ISMB (Supplement of Bioinformatics), 2006)

A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs. - Giovanni Bottegoni; Andrea Cavalli; Maurizio Recanatini (J. Chem. Inf. Model., 2006)

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). - Giovanni Bottegoni; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2008)

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. - Manuel Rueda; Giovanni Bottegoni; Ruben Abagyan (J. Chem. Inf. Model., 2009)

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. - Manuel Rueda; Giovanni Bottegoni; Ruben Abagyan (J. Chem. Inf. Model., 2010)

SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design. - Angelo D. Favia; Giovanni Bottegoni; Irene Nobeli; Paola Bisignano; Andrea Cavalli (J. Chem. Inf. Model., 2011)

Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design. - Puneet Kacker; Matteo Masetti; Martina Mangold; Giovanni Bottegoni; Andrea Cavalli (J. Chem. Inf. Model., 2012)

Structure-Based Predictions of Activity Cliffs. - Jarmila Husby; Giovanni Bottegoni; Irina Kufareva; Ruben Abagyan; Andrea Cavalli (J. Chem. Inf. Model., 2015)

BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. - Sergio Decherchi; Giovanni Bottegoni; Andrea Spitaleri; Walter Rocchia; Andrea Cavalli (J. Chem. Inf. Model., 2018)

Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. - Sergio Decherchi; Giovanni Bottegoni; Andrea Spitaleri; Walter Rocchia; Andrea Cavalli (J. Chem. Inf. Model., 2018)

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential. - Sonja Peter; Lydia Siragusa; Morgan Thomas; Tommaso Palomba; Simon Cross; Noel M. O'Boyle; Dávid Bajusz; György G. Ferenczy; György M. Keserü; Giovanni Bottegoni; Brian Joseph Bender; I-Jen Chen; et al. (J. Chem. Inf. Model., 2024)

Adiabatic-Bias Molecular Dynamics Simulations Reveal the Impact of Mutations on Muscarinic Antagonist Unbinding Kinetics. - Adriana Coricello; Anna Lisa Chiaravalle; Maria Musgaard; Benjamin Gerald Tehan; Gian Marco Elisi; Giovanni Bottegoni (J. Chem. Inf. Model., 2025)

Application of Deep Learning to Predict the Persistence, Bioaccumulation, and Toxicity of Pharmaceuticals. - Dominga Evangelista; Elliot Nelson; Rachael Skyner; Ben Tehan; Mattia Bernetti; Marinella Roberti; Maria Laura Bolognesi; Giovanni Bottegoni (J. Chem. Inf. Model., 2025)