Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set von Lenselink, Eelke B., ten Dijke, Niels, Bongers, Brandon, Papadatos, George, van Vlijmen, Herman W. T., Kowalczyk, Wojtek, IJzerman, Adriaan P., van Westen, Gerard J. P.

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An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor von Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.

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DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology von Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., Emmerich, Michael T. M., IJzerman, Adriaan P., van Westen, Gerard J. P.

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Quantitative prediction of selectivity between the A1 and A2A adenosine receptors von Burggraaff, Lindsey, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.

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Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development von van Westen, Gerard J P, Wegner, Jörg K, Geluykens, Peggy, Kwanten, Leen, Vereycken, Inge, Peeters, Anik, Ijzerman, Adriaan P, van Vlijmen, Herman W T, Bender, Andreas

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Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling von Burggraaff, Lindsey, Oranje, Paul, Gouka, Robin, van der Pijl, Pieter, Geldof, Marian, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.

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DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning von Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.

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Trends in Antibody Sequence Changes during the Somatic Hypermutation Process von Clark, Louis A, Ganesan, Skanth, Papp, Sarah, van Vlijmen, Herman W. T

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Advances and Challenges in Computational Target Prediction von Sydow, Dominique, Burggraaff, Lindsey, Szengel, Angelika, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P, Volkamer, Andrea

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Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data von van Westen, Gerard J P, Hendriks, Alwin, Wegner, Jörg K, Ijzerman, Adriaan P, van Vlijmen, Herman W T, Bender, Andreas

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Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation von Lenselink, Eelke B, Louvel, Julien, Forti, Anna F, van Veldhoven, Jacobus P. D, de Vries, Henk, Mulder-Krieger, Thea, McRobb, Fiona M, Negri, Ana, Goose, Joseph, Abel, Robert, van Vlijmen, Herman W. T, Wang, Lingle, Harder, Edward, Sherman, Woody, IJzerman, Adriaan P, Beuming, Thijs

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Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation von Deflorian, Francesca, Perez-Benito, Laura, Lenselink, Eelke B, Congreve, Miles, van Vlijmen, Herman W. T, Mason, Jonathan S, Graaf, Chris de, Tresadern, Gary

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Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases von Koldenhof, Patrick, Bemelmans, Martijn P., Ghosh, Brahma, Damm‐Ganamet, Kelly L., Vlijmen, Herman W. T., Pande, Vineet

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Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study von Keränen, Henrik, Pérez-Benito, Laura, Ciordia, Myriam, Delgado, Francisca, Steinbrecher, Thomas B, Oehlrich, Daniel, van Vlijmen, Herman W. T, Trabanco, Andrés A, Tresadern, Gary

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Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery von Sabanés Zariquiey, Francesc, Jacoby, Edgar, Vos, Ann, van Vlijmen, Herman W. T, Tresadern, Gary, Harvey, Jeremy

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Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs von Burggraaff, Lindsey, van Veen, Amber, Lam, Chi Chung, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P

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A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization von van der Horst, Eelke, Peironcely, Julio E, Ijzerman, Adriaan P, Beukers, Margot W, Lane, Jonathan R, van Vlijmen, Herman W T, Emmerich, Michael T M, Okuno, Yasushi, Bender, Andreas

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Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling von Tresadern, Gary, Trabanco, Andres A, Pérez-Benito, Laura, Overington, John P, van Vlijmen, Herman W. T, van Westen, Gerard J. P

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Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors von Burggraaff, Lindsey, Lenselink, Eelke B, Jespers, Willem, van Engelen, Jesper, Bongers, Brandon J, González, Marina Gorostiola, Liu, Rongfang, Hoos, Holger H, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P

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Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets von van Westen, Gerard J. P, Wegner, Jörg K, IJzerman, Adriaan P, van Vlijmen, Herman W. T, Bender, A

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