Charge transfer mechanism in a PolydGpdCp fiber and in wet DNA. - Francesco Luigi Gervasio (Comput. Phys. Commun., 2007)

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. - Inés G. Muñoz; Jesús Prieto; Sunita Subramanian; Javier Coloma; Pilar Redondo; Maider Villate; Nekane Merino; Marco Marenchino; Marco D'Abramo; Francesco L. Gervasio; Sylvestre Grizot; Fayza Daboussi; et al. (Nucleic Acids Res., 2011)

The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion. - Nicole Dölker; Maria W. Górna; Ludovico Sutto; Antonio S. Torralba; Giulio Superti-Furga; Francesco L. Gervasio (PLoS Comput. Biol., 2014)

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics. - Silvia Lovera; Maria Morando; Encarna Pucheta-Martinez; Jorge L. Martinez-Torrecuadrada; Giorgio Saladino; Francesco L. Gervasio (PLoS Comput. Biol., 2015)

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. - Noureldin Saleh; Passainte Ibrahim; Giorgio Saladino; Francesco L. Gervasio; Timothy Clark (J. Chem. Inf. Model., 2017)

Understanding Ligand Binding Selectivity in a Prototypical GPCR Family. - Giulio Mattedi; Francesca Deflorian; Jonathan S. Mason; Chris de Graaf; Francesco L. Gervasio (J. Chem. Inf. Model., 2019)

BioSimSpace: An interoperable Python framework for biomolecular simulation. - Lester O. Hedges; Antonia S. J. S. Mey; Charles A. Laughton; Francesco L. Gervasio; Adrian J. Mulholland; Christopher J. Woods; Julien Michel (J. Open Source Softw., 2019)

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses. - Dominykas Lukauskis; Marley L. Samways; Simone Aureli; Benjamin P. Cossins; Richard D. Taylor; Francesco Luigi Gervasio (J. Chem. Inf. Model., 2022)

General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. - Jacqueline C. Calderón; Passainte Ibrahim; Dorothea Gobbo; Francesco Luigi Gervasio; Timothy Clark (J. Chem. Inf. Model., 2023)

Activation/Deactivation Free-Energy Profiles for the β2-Adrenergic Receptor: Ligand Modes of Action. - Jacqueline C. Calderón; Passainte Ibrahim; Dorothea Gobbo; Francesco Luigi Gervasio; Timothy Clark (J. Chem. Inf. Model., 2023)

Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study. - Simone Aureli; Francesco Bellina; Valerio Rizzi; Francesco Luigi Gervasio (J. Chem. Inf. Model., 2024)

Determinants of Neutral Antagonism and Inverse Agonism in the β2-Adrenergic Receptor. - Jacqueline C. Calderón; Passainte Ibrahim; Dorothea Gobbo; Francesco Luigi Gervasio; Timothy Clark (J. Chem. Inf. Model., 2024)

Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. - Jacqueline C. Calderón; Eva Plut; Max Keller; Chiara Cabrele; Oliver Reiser; Francesco L. Gervasio; Timothy Clark (J. Chem. Inf. Model., 2024)

Learning committor-consistent collective variables. - Thorben Fröhlking; Simone Aureli; Francesco Luigi Gervasio (Nat. Comput. Sci., 2025)