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Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-dimensional optimization2025 Nature Communications article Computer Science Computational Drug Discovery Methods Open access
David F. Nippa, Kenneth Atz, Yannick Stenzhorn, Alex T. Müller, Andreas Tosstorff, Jörg Benz, +17 more
9citations -
Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design2025 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Helle W. van den Maagdenberg, Jikke de Mol van Otterloo, J. G. Coen van Hasselt, Piet H. van der Graaf, Gerard J. P. van Westen
12citations -
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease2021 Scientific Reports article Computer Science Computational Drug Discovery Methods Open access cited by 1 patent
Michael G. Sugiyama, Haotian Cui, Dar’ya S. Redka, Mehran Karimzadeh, Edurne Rujas, Hassaan Maan, +16 more
27citations -
In Search of Beautiful Molecules: A Perspective on Generative Modeling for Drug Design2025 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Remco L. van den Broek, Shivam Patel, Gerard J. P. van Westen, Willem Jespers, Woody Sherman
37citations -
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology2021 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access cited by 1 patent
Xuhan Liu, Kai Ye, Herman van Vlijmen, Michael Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen
118citations -
DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space2023 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Martin Šícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen
40citations -
Knowledge Graphs and Explainable Artificial Intelligence (AI) for Drug Repurposing on Rare Diseases2026 Neurosymbolic Artificial Intelligence article Computer Science Computational Drug Discovery Methods Open access
Pablo Perdomo-Quinteiro, Katherine Wolstencroft, Marco Roos, Núria Queralt-Rosiñach
0citations -
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design2025 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access
Alan Kai Hassen, Martin Šícho, Yorick J. van Aalst, Mirjam C. W. Huizenga, Darcy N. R. Reynolds, Sohvi Luukkonen, +5 more
15citations -
Stratification and prediction of drug synergy based on target functional similarity2020 npj Systems Biology and Applications article Computer Science Computational Drug Discovery Methods Open access
Mi Yang, Patricia Jaaks, Jonathan R. Dry, Mathew J. Garnett, Michael P. Menden, Julio Sáez-Rodríguez
60citations -
Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE2020 PLoS Computational Biology article Computer Science Computational Drug Discovery Methods Open access cited by 1 patent
Lisa-Katrin Schätzle, Ali Hadizadeh Esfahani, Andreas Schuppert
16citations -
Structure-Based Discovery of Mouse Trace Amine-Associated Receptor 5 Antagonists2023 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Alessandro Nicoli, Verena Weber, Carlotta Bon, Alexandra Steuer, Stefano Gustincich, Raul R. Gainetdinov, +3 more
7citations -
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 -
AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models2024 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Andrius Bernatavicius, Martin Šícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuß, Gerard J. P. van Westen
20citations