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Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution2022 Frontiers in Cell and Developmental Biology article Computer Science Computational Drug Discovery Methods Open access
Gia Linh Hoang, Jonas Goßen, Riccardo Capelli, Toan T. Nguyen, Zhaoxi Sun, Ke Zuo, +3 more
6citations -
Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein–Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors2021 Journal of Chemical Theory and Computation article Computer Science Computational Drug Discovery Methods Open access
Qianqian Zhao, Riccardo Capelli, Paolo Carloni, Bernhard Lüscher, Jinyu Li, Giulia Rossetti
28citations -
Metadynamics simulations of ligands binding to protein surfaces: a novel tool for rational drug design2023 Physical Chemistry Chemical Physics article Computer Science Computational Drug Discovery Methods Open access
Ke Zuo, Agata Kranjc, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni
16citations -
Structural Determinants of Mac1 Inhibition: Lessons from Ligand Binding Patterns2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Computational Drug Discovery Methods Open access
Verena Weber, Giulia Rossetti, Bernhard Lüscher, Patricia Korn, Sarah Knapp
0citations -
Structural Determinants of Mac1 Inhibition: Lessons from Ligand Binding Patterns2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Computational Drug Discovery Methods Open access
Verena Weber, Giulia Rossetti, Bernhard Lüscher, Patricia Korn, Sarah Knapp
0citations -
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET2023 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni
8citations -
Fi-score: a novel approach to characterise protein topology and aid in drug discovery studies2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access
Austė Kanapeckaitė, Claudia Beaurivage, MATTHEW J. HANCOCK, Erik Verschueren
2citations -
Navigating the complexities of docking tools with nicotinic receptors and acetylcholine binding proteins in the realm of neonicotinoids2024 Ecotoxicology and Environmental Safety article Computer Science Computational Drug Discovery Methods Open access
Zakaria Bouchouireb, Damien Olivier‐Jimenez, Titouan Jaunet‐Lahary, Steeve Hervé Thany, Jean‐Yves Le Questel
14citations -
A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access
Jonas Goßen, Simone Albani, Anton Hanke, Benjamin Philipp Joseph, Cathrine C. Bergh, Maria Kuzikov, +14 more
5citations -
Machine Learning-aided Discovery of Novel Chemotype Antagonists for G Protein-coupled Receptors: The Case of the Adenosine A 2A Receptor2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access
Jonas Goßen, Rui Pedro Ribeiro, Dirk DB Bier, Bernd Neumaier, Paolo Carloni, Alejandro Giorgetti, +1 more
2citations -
Multimap Targeted Free Energy Estimation: A Mechanical Embedding QM/MM Scheme For Protein-Ligand Affinities2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Computational Drug Discovery Methods Open access
Jacques Gay, Andrea Rizzi, Shina Caroline Lynn Kamerlin, Davide Mandelli, Paolo Carloni
0citations -
Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site2026 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
David Alencar Araripe, Alejandro Díaz‐Holguín, Antti Poso, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez‐de‐Terán, +1 more
3citations -
Large-Scale Modeling of Sparse Protein Kinase Activity Data2023 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Sohvi Luukkonen, Erik Meijer, Giovanni A. Tricarico, Johan Hofmans, Pieter F. W. Stouten, Gerard J. P. van Westen, +1 more
14citations