Gerard J. P. van Westen

53 papers Journal 52

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site. J. Chem. Inf. Model. David Alencar Araripe, Alejandro Díaz-Holguín, Antti Poso, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán, Willem Jespers
2026	J	`jnl`	PyTEA-O: a Python implementation of Two-Entropies Analysis for protein sequence variation analysis. Bioinform. Rosan C. M. Kuin, Alexander T. Julian, Jagriti Chander, Sunah Lee, Gerard J. P. van Westen
2025	J	`jnl`	Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstration. CoRR Alan Kai Hassen, Andrius Bernatavicius, Antonius P. A. Janssen, Mike Preuss, Gerard J. P. van Westen, Djork-Arné Clevert
2025	J	`jnl`	Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists. J. Chem. Inf. Model. Khaled Essa, Kian Noorman van der Dussen, Yao Yao, Bente Bleijs, Natalia V. Ortiz Zacarias, Laura H. Heitman, Gerard J. P. van Westen, Willem Jespers, Daan van der Es, Martin Sícho
2025	J	`jnl`	Combining Bayesian and Evidential Uncertainty Quantification for Improved Bioactivity Modeling. J. Chem. Inf. Model. Bola Khalil, Kajetan Schweighofer, Natalia Dyubankova, Gerard J. P. van Westen, Herman van Vlijmen
2025	J	`jnl`	Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design. J. Cheminformatics Alan Kai Hassen, Martin Sícho, Yorick J. van Aalst, Mirjam C. W. Huizenga, Darcy N. R. Reynolds, Sohvi Luukkonen, Andrius Bernatavicius, Djork-Arné Clevert, Antonius P. A. Janssen, Gerard J. P. van Westen, Mike Preuss
2025	J	`jnl`	In Search of Beautiful Molecules: A Perspective on Generative Modeling for Drug Design. J. Chem. Inf. Model. Remco L. van den Broek, Shivam Patel, Gerard J. P. van Westen, Willem Jespers, Woody Sherman
2025	J	`jnl`	Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design. J. Chem. Inf. Model. 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
2025	J	`jnl`	PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries. Bioinform. Rosan C. M. Kuin, Meindert H. Lamers, Gerard J. P. van Westen
2025	J	`jnl`	Toward Assay-Aware Bioactivity Model(er)s: Getting a Grip on Biological Context. J. Chem. Inf. Model. Linde Schoenmaker, Enzo G. Sastrokarijo, Laura H. Heitman, Joost B. Beltman, Willem Jespers, Gerard J. P. van Westen
2024	J	`jnl`	AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models. J. Chem. Inf. Model. Andrius Bernatavicius, Martin Sícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuss, Gerard J. P. van Westen
2024	J	`jnl`	Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell. Bioinform. Remco L. van den Broek, Xabier Bello, Rebecca V. Küpper, Gerard J. P. van Westen, Willem Jespers, Hugo Gutiérrez-de-Terán
2024	J	`jnl`	QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool. J. Cheminformatics Helle W. van den Maagdenberg, Martin Sícho, David Alencar Araripe, Sohvi Luukkonen, Linde Schoenmaker, Michiel Jespers, Olivier J. M. Béquignon, Marina Gorostiola González, Remco L. van den Broek, Andrius Bernatavicius, J. G. Coen van Hasselt, Piet H. Van Der Graaf, Gerard J. P. van Westen
2023	J	`jnl`	3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors. J. Cheminformatics Marina Gorostiola González, Remco L. van den Broek, Thomas G. M. Braun, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen
2023	J	`jnl`	Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells. J. Chem. Inf. Model. Olivier J. M. Béquignon, José Carlos Gómez-Tamayo, Eelke B. Lenselink, Steven Wink, Steven Hiemstra, Chi Chung Lam, Domenico Gadaleta, Alessandra Roncaglioni, Ulf Norinder, Bob van de Water, Manuel Pastor, Gerard J. P. van Westen
2023	J	`jnl`	DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. J. Cheminformatics Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2023	J	`jnl`	DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. J. Chem. Inf. Model. Martin Sícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen
2023	J	`jnl`	Large-Scale Modeling of Sparse Protein Kinase Activity Data. J. Chem. Inf. Model. Sohvi Luukkonen, Erik Meijer, Giovanni Tricarico, Johan Hofmans, Pieter F. W. Stouten, Gerard J. P. van Westen, Eelke B. Lenselink
2023	J	`jnl`	Papyrus: a large-scale curated dataset aimed at bioactivity predictions. J. Cheminformatics Olivier J. M. Béquignon, Brandon J. Bongers, Willem Jespers, Adriaan P. IJzerman, B. van der Water, Gerard J. P. van Westen
2023	J	`jnl`	Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. J. Chem. Inf. Model. Brandon J. Bongers, Huub J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen
2023	J	`jnl`	UnCorrupt SMILES: a novel approach to de novo design. J. Cheminformatics Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers, Gerard J. P. van Westen
2022	J	`jnl`	Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening. J. Chem. Inf. Model. Alzbeta Türková, Brandon J. Bongers, Ulf Norinder, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, Gergely Szakács, Csilla Özvegy-Laczka, Gerard J. P. van Westen, Barbara Zdrazil
2021	—	`ch.`	Computational Approaches for De Novo Drug Design: Past, Present, and Future. Artificial Neural Networks, 3rd Edition Xuhan Liu, Adriaan P. IJzerman, Gerard J. P. van Westen
2021	J	`jnl`	Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. PLoS Comput. Biol. Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán
2021	J	`jnl`	DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. J. Cheminformatics Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen
2021	J	`jnl`	GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. J. Cheminformatics Martin Sícho, Xuhan Liu, Daniel Svozil, Gerard J. P. van Westen
2020	J	`jnl`	Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. J. Chem. Inf. Model. Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2020	J	`jnl`	QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. J. Cheminformatics Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil
2020	J	`jnl`	Quantitative prediction of selectivity between the A J. Cheminformatics Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2020	J	`jnl`	Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. J. Chem. Inf. Model. Lindsey Burggraaff, Eelke B. Lenselink, Willem Jespers, Jesper E. van Engelen, Brandon J. Bongers, Marina Gorostiola González, Rongfang Liu, Holger H. Hoos, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2019	J	`jnl`	A multiple classifier system identifies novel cannabinoid CB2 receptor ligands. J. Cheminformatics David Ruano-Ordás, Lindsey Burggraaff, Rongfang Liu, Cas van der Horst, Laura H. Heitman, Michael T. M. Emmerich, José Ramón Méndez, Iryna Yevseyeva, Gerard J. P. van Westen
2019	J	`jnl`	Advances and Challenges in Computational Target Prediction. J. Chem. Inf. Model. Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer
2019	J	`jnl`	An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. J. Cheminformatics Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2019	J	`jnl`	Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes. J. Chem. Inf. Model. Antonius P. A. Janssen, Sebastian H. Grimm, Ruud H. M. Wijdeven, Eelke B. Lenselink, Jacques Neefjes, Constant A. A. van Boeckel, Gerard J. P. van Westen, Mario van der Stelt
2019	J	`jnl`	Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. J. Cheminformatics Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2018	J	`jnl`	Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings Bioinform. Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen
2017	J	`jnl`	Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. J. Cheminformatics Eelke B. Lenselink, Niels ten Dijke, Brandon J. Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, Gerard J. P. van Westen
2017	J	`jnl`	Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. J. Chem. Inf. Model. Gary Tresadern, Andrés A. Trabanco, Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, Gerard J. P. van Westen
2016	J	`jnl`	Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinform. Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin
2016	J	`jnl`	Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. J. Chem. Inf. Model. Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2016	J	`jnl`	Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? J. Chem. Inf. Model. Serge Christmann-Franck, Gerard J. P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, Daniel Domine
2015	J	`jnl`	Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. BMC Bioinform. Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin
2015	J	`jnl`	Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. J. Cheminformatics Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen
2015	J	`jnl`	Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. J. Cheminformatics Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin
2014	J	`jnl`	A document classifier for medicinal chemistry publications trained on the ChEMBL corpus. J. Cheminformatics George Papadatos, Gerard J. P. van Westen, Samuel Croset, Rita Santos, Simone Trubian, John P. Overington
2014	J	`jnl`	Chemical, Target, and Bioactive Properties of Allosteric Modulation. PLoS Comput. Biol. Gerard J. P. van Westen, Anna Gaulton, John P. Overington
2014	J	`jnl`	Proteochemometric modeling in a Bayesian framework. J. Cheminformatics Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin
2013	J	`jnl`	Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. J. Cheminformatics Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2013	J	`jnl`	Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics Gerard J. P. van Westen, Remco F. Swier, Isidro Cortes-Ciriano, Jörg K. Wegner, John P. Overington, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2013	J	`jnl`	Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. PLoS Comput. Biol. Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2010	J	`jnl`	Molecular bioactivity extrapolation to novel targets by support vector machines. J. Cheminformatics Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2010	J	`jnl`	Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models. J. Cheminformatics Olaf van den Hoven, Gerard J. P. van Westen, Andreas Bender
2009	J	`jnl`	Chemogenomics: Looking at biology through the lens of chemistry. Stat. Anal. Data Min. Munikumar R. Doddareddy, Gerard J. P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. IJzerman, Michael Emmerich, Jeremy L. Jenkins, Andreas Bender