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Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation2020 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods cited by 4 patents
Francesca Deflorian, Laura Pérez‐Benito, Eelke Bart Lenselink, Miles Congreve, Herman van Vlijmen, Jonathan S. Mason, +2 more
88citations -
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 -
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 -
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by Free Energy simulations2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Willem Jespers, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Åqvist, Hugo Gutiérrez‐de‐Terán
0citations -
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 -
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations2021 PLoS Computational Biology article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, +1 more
9citations -
Fine tuning of long-range interactions to describe the binding of adamantane and diamantane derivatives to a Cucurbit[7]uril-based synthetic receptor: Insights from metadynamics simulations2025 The Journal of Chemical Physics article Chemistry Supramolecular Chemistry and Complexes Open access
Amal Vijay, Giacomo Salvadori, Frank Biedermann, Giulia Rossetti, Paolo Carloni, Davide Mandelli
0citations -
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 -
Rational Design Yields Molecular Insights on Leaf-Binding of Anchor Peptides2022 ACS Applied Materials & Interfaces article Materials Science Polymer Surface Interaction Studies
Jonas Dittrich, Christin Brethauer, L.A. GONCHARENKO, Jens Bührmann, Viktoria Valeska Zeisler-Diehl, Shyam Pariyar, +5 more
20citations -
Overview on Building Blocks and Applications of Efficient and Robust Extended Tight Binding2025 The Journal of Physical Chemistry A article Physics and Astronomy Advanced Chemical Physics Studies Open access
Abylay Katbashev, Marcel Stahn, Thomas Rose, Vahideh Alizadeh, Marvin Friede, Christoph Plett, +2 more
25citations -
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 -
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 -
Oseltamivir aziridines are potent influenza neuraminidase inhibitors and imaging agents2026 Proceedings of the National Academy of Sciences article Medicine Influenza Virus Research Studies Open access
Merijn B. L. Vriends, E. J. MORAN, Martín Calvelo, Thomas Ross Hansen, Isabelle B. Pickles, Xincheng Xin, +17 more
2citations -
Identification of V6.51L as a selectivity hotspot in stereoselective A2B adenosine receptor antagonist recognition2021 Scientific Reports article Biochemistry, Genetics and Molecular Biology Adenosine and Purinergic Signaling Open access
Xuesong Wang, Willem Jespers, Rubén Prieto‐Díaz, María Majellaro, Adriaan P. IJzerman, Gerard J. P. van Westen, +3 more
14citations -
Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell2024 Bioinformatics article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Remco L. van den Broek, Xabier Bello, Rebecca V Küpper, Gerard J. P. van Westen, Willem Jespers, Hugo Gutiérrez‐de‐Terán
5citations -
Minimally modified human blood coagulation factor X to bypass direct factor Xa inhibitors2024 Journal of Thrombosis and Haemostasis article Medicine Blood Coagulation and Thrombosis Mechanisms Open access cited by 1 patent
Mark Schreuder, Georges Jourdi, Dejvid Veizaj, David Alonzo Poole III, Ka Lei Cheung, Géraldine Poénou, +10 more
5citations -
Ligand Affinities within the Open-Boundary Molecular Mechanics/Coarse-Grained Framework (I): Alchemical Transformations within the Hamiltonian Adaptive Resolution Scheme3citations