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A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics2021 ACS Pharmacology & Translational Science article Computer Science Computational Drug Discovery Methods Open access
Jonas Goßen, Simone Albani, Anton Hanke, Benjamin Philipp Joseph, Cathrine C. Bergh, Maria Kuzikov, +14 more
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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
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Physical pooling functions in graph neural networks for molecular property prediction2023 Computers & Chemical Engineering article Computer Science Computational Drug Discovery Methods Open access
Artur M. Schweidtmann, Jan G. Rittig, Jana M. Weber, Martin Grohe, Manuel Dahmen, Kai O. Leonhard, +1 more
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The Bigger Fish: A Comparison of Meta-Learning QSAR Models on Low-Resourced Aquatic Toxicity Regression Tasks2023 Environmental Science & Technology article Computer Science Computational Drug Discovery Methods Open access
Thalea Schlender, Markus Viljanen, Jan N. van Rijn, Felix Mohr, Willie J.G.M. Peijnenburg, Holger H. Hoos, +2 more
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Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers2021 arXiv (Cornell University) preprint Computer Science Computational Drug Discovery Methods Open access
Agastya P. Bhati, Shunzhou Wan, Austin Clyde, Mathis Bode, Mikhail Titov, André Merzky, +20 more
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Systematic evaluation of high-throughput PBK modelling strategies for the prediction of intravenous and oral pharmacokinetics in humans2024 Archives of Toxicology article Computer Science Computational Drug Discovery Methods Open access
René Geci, Domenico Gadaleta, Marina García de Lomana, Rita Ortega-Vallbona, Erika Colombo, Eva Serrano‐Candelas, +3 more
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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 -
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson2022 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access
Jan C. Brammer, Gerd Blanke, Claudia Kellner, Alexander Hoffmann, Sonja Herres‐Pawlis, Ulrich Schatzschneider
27citations -
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
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Expanding the boundaries of ligand–target modeling by exascale calculations2021 Wiley Interdisciplinary Reviews Computational Molecular Science article Computer Science Computational Drug Discovery Methods Open access
Viacheslav Bolnykh, Giulia Rossetti, Ursula Röthlisberger, Paolo Carloni
19citations -
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 -
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
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Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach2020 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods
Ksenia Korshunova, Zeineb Si Chaib, Alejandro Giorgetti, Mercedes Alfonso‐Prieto, Paolo Carloni
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Solvation Free Energies of Anions: From Curated Reference Data to Predictive Models2025 Journal of the American Chemical Society article Computer Science Computational Drug Discovery Methods Open access
Thomas Nevolianis, Jonathan Wenyuan Zheng, Simon Müller, Matthias Baumann, Sofja Tshepelevitsh, Ivari Kaljurand, +4 more
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Mechanism Research of Chonglou as a Pain Killer by Network Pharmacology2021 World Journal of Traditional Chinese Medicine article Computer Science Computational Drug Discovery Methods Open access
Yu‐Tong Liu, Yongli Situ, Tingting Zhao, Hekun Zeng, Shang-Dong Liang, Günther Schmalzing, +4 more
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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