Structural models of human big conductance calcium- and voltage-gated potassium channels. - Agata Kranjc; Claudio Anselmi; Paolo Carloni; Frank E. Blaney (Comput. Phys. Commun., 2007)

On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study. - V. Carnevale; Simone Raugei; Simone Piana; Paolo Carloni (Comput. Phys. Commun., 2008)

Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure. - Katrin Spiegel; Alessandra Magistrato; Patrick Maurer; Paolo Ruggerone; Ursula Rothlisberger; Paolo Carloni; Jan Reedijk; Michael L. Klein (J. Comput. Chem., 2008)

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations. - Vanessa Leone; Gianluca Lattanzi; Carla Molteni; Paolo Carloni (PLoS Comput. Biol., 2009)

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions. - Roberto Marchese; Rita Grandori; Paolo Carloni; Simone Raugei (PLoS Comput. Biol., 2010)

Molecular motions in drug design: the coming age of the metadynamics method. - Xevi Biarnés; Salvatore Bongarzone; Attilio Vittorio Vargiu; Paolo Carloni; Paolo Ruggerone (J. Comput. Aided Mol. Des., 2011)

On the active site of mononuclear B1 metallo β-lactamases: a computational study. - Jacopo Sgrignani; Alessandra Magistrato; Matteo Dal Peraro; Alejandro J. Vila; Paolo Carloni; Roberta Pierattelli (J. Comput. Aided Mol. Des., 2012)

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer. - Jinyu Li 005; Giulia Rossetti; Jens Dreyer; Simone Raugei; Emiliano Ippoliti; Bernhard Lüscher; Paolo Carloni (PLoS Comput. Biol., 2014)

Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant. - Jinyu Li 005; Jörg Vervoorts; Paolo Carloni; Giulia Rossetti; Bernhard Lüscher (BMC Bioinform., 2017)

Unifying view of mechanical and functional hotspots across class A GPCRs. - Luca Ponzoni; Giulia Rossetti; Luca Maggi; Alejandro Giorgetti; Paolo Carloni; Cristian Micheletti (PLoS Comput. Biol., 2017)

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. - Anna Bochicchio; Miroslav Krepl; Fan Yang; Gabriele Varani; Jirí Sponer; Paolo Carloni (PLoS Comput. Biol., 2018)

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals. - Neil J. Bruce; Daniele Narzi; Daniel Trpevski; Siri Camee van Keulen; Anu G. Nair; Ursula Rothlisberger; Rebecca C. Wade; Paolo Carloni; Jeanette Hellgren Kotaleski (PLoS Comput. Biol., 2019)

Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. - Jakob Schneider; Ksenia Korshunova; Zeineb Si Chaib; Alejandro Giorgetti; Mercedes Alfonso-Prieto; Paolo Carloni (J. Chem. Inf. Model., 2020)

Scalability of 3D-DFT by block tensor-matrix multiplication on the JUWELS Cluster. - Nitin Malapally; Viacheslav Bolnykh; Estela Suarez; Paolo Carloni; Thomas Lippert; Davide Mandelli (CoRR, 2023)

Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. - Mirko Paulikat; Daniele Vitone; Florian Karl Schackert; Nils Schuth; Alessandra Barbanente; GiovanniMaria Piccini; Emiliano Ippoliti; Giulia Rossetti; Adam H. Clark; Maarten Nachtegaal; Michael Haumann; Holger Dau; et al. (J. Chem. Inf. Model., 2023)

Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. - Ke Zuo; Riccardo Capelli; Giulia Rossetti; Rachel Nechushtai; Paolo Carloni (J. Chem. Inf. Model., 2023)

Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. - Florian Karl Schackert; Johann Biedermann; Saeid Abdolvand; Sonja Minniberger; Chen Song; Andrew J. R. Plested; Paolo Carloni; Han Sun (J. Chem. Inf. Model., 2023)

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations. - Bharath Raghavan; Florian K. Schackert; Andrea Levy; Sophia K. Johnson; Emiliano Ippoliti; Davide Mandelli; Jógvan Magnus Haugaard Olsen; Ursula Rothlisberger; Paolo Carloni (J. Chem. Inf. Model., 2023)

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)

Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail. - Mirko Paulikat; GiovanniMaria Piccini; Emiliano Ippoliti; Giulia Rossetti; Fabio Arnesano; Paolo Carloni (J. Chem. Inf. Model., 2023)

Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. - Simone Albani; Elisa Costanzi; Gia Linh Hoang; Maria Kuzikov; Marcus Frings; Narjes Ansari; Nicola Demitri; Toan T. Nguyen; Valerio Rizzi; Jörg B. Schulz; Carsten Bolm; Andrea Zaliani; et al. (J. Chem. Inf. Model., 2024)

Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution. - Emile de Bruyn; Anton Emil Dorn; Giulia Rossetti; Claudio Fernandez; Tiago F. Outeiro; Jörg B. Schulz; Paolo Carloni (J. Chem. Inf. Model., 2024)

3D DFT by block tensor-matrix multiplication via a modified Cannon's algorithm: Implementation and scaling on distributed-memory clusters with fat tree networks. - Nitin Malapally; Viacheslav Bolnykh; Estela Suarez; Paolo Carloni; Thomas Lippert; Davide Mandelli (J. Parallel Distributed Comput., 2024)

Role of Residues Undergoing Hereditary Spastic Paraplegias Mutations: Insights from Simulating the Spiral to Ring Transition in Katanin. - Maria S. Kelly; Riccardo Capelli; Ruxandra I. Dima; Paolo Carloni (J. Chem. Inf. Model., 2025)

Impact of Genetic Variants Associated with Neurodevelopmental Disorders on the WAVE Regulatory Complex. - Song Xie; Ke Zuo; Silvia De Rubeis; Giorgio Bonollo; Giorgio Colombo 001; Paolo Ruggerone; Paolo Carloni (J. Chem. Inf. Model., 2025)