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Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices2022 Angewandte Chemie International Edition article Computer Science Research Data Management Practices Open access
Sonja Herres‐Pawlis, Felix Bach, Ian J. Bruno, Stuart J. Chalk, Nicole Jung, Johannes C. Liermann, +5 more
39citations -
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 -
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 -
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
43citations -
Toward Assay-Aware Bioactivity Model(er)s: Getting a Grip on Biological Context2025 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Linde Schoenmaker, Enzo G. Sastrokarijo, Laura H. Heitman, Joost B. Beltman, Willem Jespers, Gerard J. P. van Westen
21citations -
Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors2023 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Brandon J. Bongers, Hubert J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, +1 more
8citations -
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 -
Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening2022 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Alzbeta Tuerkova, Brandon J. Bongers, Ulf Norinder, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, +4 more
24citations -
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors2020 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Lindsey Burggraaff, Eelke Bart Lenselink, Willem Jespers, Jesper E. van Engelen, Brandon J. Bongers, Marina Gorostiola González, +5 more
13citations -
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 -
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs2020 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
10citations -
Combining Bayesian and Evidential Uncertainty Quantification for Improved Bioactivity Modeling2025 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Kajetan Schweighofer, Natalia Dyubankova, Gerard J. P. van Westen, Herman van Vlijmen
8citations -
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 -
Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials2022 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Bregje W. Brinkmann, Ankush Singhal, G. J. A. Sevink, Lisette Neeft, Martina G. Vijver, Willie J.G.M. Peijnenburg
7citations -
Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells2023 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Olivier J. M. Béquignon, José Carlos Gómez-Tamayo, Eelke Bart Lenselink, Steven Wink, Steven W. Hiemstra, Chi Chung Lam, +6 more
3citations -
Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists2025 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Khaled Essa, Kian Noorman van der Dussen, Yao Yao, Bente T.M. Bleijs, Natalia V. Ortiz Zacarı́as, Laura H. Heitman, +4 more
1citations -
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 -
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
16citations -
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 -
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