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Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding2025 The Journal of Physical Chemistry B article Computer Science Computational Drug Discovery Methods Open access
Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M. Rangwala, Jessica B. White, +10 more
15citations -
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 -
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 -
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 -
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 -
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 -
Prediction models for hormone receptor status in female breast cancer do not extend to males: further evidence of sex-based disparity in breast cancer
Subarnarekha Chatterji, Marko van Treeck, Chiara Maria Lavinia Loeffler, Oliver Lester Saldanha, Gregory Patrick Veldhuizen, Didem Çifçi, +4 more
8citations -
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 -
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 -
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 -
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 -
Identification of mitochondrial toxicants by combined in silico and in vitro studies – A structure-based view on the adverse outcome pathway2020 Computational Toxicology article Computer Science Computational Drug Discovery Methods Open access
Florentina Troger, Johannes Delp, Melina Funke, Wanda van der Stel, Claire Colas, Marcel Leist, +2 more
22citations -
Refining Ligand Poses in RNA/Ligand Complexes of Pharmaceutical Relevance: A Perspective by QM/MM Simulations and NMR Measurements2025 The Journal of Physical Chemistry Letters article Computer Science Computational Drug Discovery Methods Open access
Gia Linh Hoang, Manuel Röck, Aldo Tancredi, Thomas Magauer, Davide Mandelli, Jörg Bernhard Schulz, +4 more
4citations -
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
38citations -
A Structure-Based Platform for Predicting Chemical-Induced Parkinson’s Disease2026 Chemical Research in Toxicology article Computer Science Computational Drug Discovery Methods Open access
Linde Schoenmaker, Emmelie van der Veer, Daan A. Jiskoot, Olivier J. M. Béquignon, Gerard J. P. van Westen, Willem Jespers
0citations -
Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses2022 Journal of the American Chemical Society article Computer Science Computational Drug Discovery Methods Open access cited by 15 patents
Andreas Luttens, Hjalmar Gullberg, Eldar Abdurakhmanov, Duy Duc Vo, Dario Akaberi, V. Talibov, +19 more
253citations