Chemogenomics: Looking at biology through the lens of chemistry. - Munikumar R. Doddareddy; Gerard J. P. van Westen; Eelke van der Horst; Julio E. Peironcely; Frans Corthals; Adriaan P. IJzerman; Michael Emmerich 001; Jeremy L. Jenkins; Andreas Bender 002 (Stat. Anal. Data Min., 2009)

Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models. - Olaf van den Hoven; Gerard J. P. van Westen; Andreas Bender 002 (J. Cheminformatics, 2010)

Molecular bioactivity extrapolation to novel targets by support vector machines. - Gerard J. P. van Westen; Jörg K. Wegner; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (J. Cheminformatics, 2010)

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. - 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 002 (J. Cheminformatics, 2013)

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. - Gerard J. P. van Westen; Remco F. Swier; Jörg K. Wegner; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (J. Cheminformatics, 2013)

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. - Gerard J. P. van Westen; Alwin Hendriks; Jörg K. Wegner; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (PLoS Comput. Biol., 2013)

Proteochemometric modeling in a Bayesian framework. - Isidro Cortes-Ciriano; Gerard J. P. van Westen; Eelke B. Lenselink; Daniel S. Murrell; Andreas Bender 002; Thérèse E. Malliavin (J. Cheminformatics, 2014)

A document classifier for medicinal chemistry publications trained on the ChEMBL corpus. - George Papadatos; Gerard J. P. van Westen; Samuel Croset; Rita Santos; Simone Trubian; John P. Overington (J. Cheminformatics, 2014)

Chemical, Target, and Bioactive Properties of Allosteric Modulation. - Gerard J. P. van Westen; Anna Gaulton; John P. Overington (PLoS Comput. Biol., 2014)

Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. - Isidro Cortes-Ciriano; Gerard J. P. van Westen; Daniel S. Murrell; Eelke B. Lenselink; Andreas Bender 002; Therese E. Malliavin (BMC Bioinform., 2015)

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. - Isidro Cortes-Ciriano; Daniel S. Murrell; Gerard J. P. van Westen; Andreas Bender 002; Thérèse E. Malliavin (J. Cheminformatics, 2015)

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. - Daniel S. Murrell; Isidro Cortes-Ciriano; Gerard J. P. van Westen; Ian Stott; Andreas Bender 002; Thérèse E. Malliavin; Robert C. Glen (J. Cheminformatics, 2015)

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. - Isidro Cortes-Ciriano; Gerard J. P. van Westen; Guillaume Bouvier; Michael Nilges; John P. Overington; Andreas Bender 002; Thérèse E. Malliavin (Bioinform., 2016)

Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? - Serge Christmann-Franck; Gerard J. P. van Westen; George Papadatos; Fanny Beltran Escudie; Alexander Roberts; John P. Overington; Daniel Domine (J. Chem. Inf. Model., 2016)

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. - Eelke B. Lenselink; Willem Jespers; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Chem. Inf. Model., 2016)

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. - 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 (J. Cheminformatics, 2017)

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. - Gary Tresadern; Andrés A. Trabanco; Laura Pérez-Benito; John P. Overington; Herman W. T. van Vlijmen; Gerard J. P. van Westen (J. Chem. Inf. Model., 2017)

Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. - Shardul Paricharak; Oscar Méndez-Lucio; Aakash Chavan Ravindranath; Andreas Bender 002; Adriaan P. IJzerman; Gerard J. P. van Westen (Briefings Bioinform., 2018)

Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. - 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 (J. Cheminformatics, 2019)

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2019)

A multiple classifier system identifies novel cannabinoid CB2 receptor ligands. - David Ruano-Ordás; Lindsey Burggraaff; Rongfang Liu; Cas van der Horst; Laura H. Heitman; Michael T. M. Emmerich; José Ramón Méndez 001; Iryna Yevseyeva; Gerard J. P. van Westen (J. Cheminformatics, 2019)

Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes. - 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 (J. Chem. Inf. Model., 2019)

Advances and Challenges in Computational Target Prediction. - Dominique Sydow; Lindsey Burggraaff; Angelika Szengel; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen; Andrea Volkamer (J. Chem. Inf. Model., 2019)

Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. - Lindsey Burggraaff; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2020)

QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. - Ctibor Skuta; Isidro Cortes-Ciriano; Wim Dehaen; Pavel Kríz; Gerard J. P. van Westen; Igor V. Tetko; Andreas Bender 002; Daniel Svozil (J. Cheminformatics, 2020)

Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. - 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 (J. Chem. Inf. Model., 2020)

Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. - Lindsey Burggraaff; Amber van Veen; Chi Chung Lam; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Chem. Inf. Model., 2020)

Computational Approaches for De Novo Drug Design: Past, Present, and Future. - Xuhan Liu; Adriaan P. IJzerman; Gerard J. P. van Westen (Artificial Neural Networks, 3rd Edition, 2021)

DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Michael T. M. Emmerich; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2021)

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. - Martin Sícho; Xuhan Liu; Daniel Svozil; Gerard J. P. van Westen (J. Cheminformatics, 2021)

Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. - Willem Jespers; Laura H. Heitman; Adriaan P. IJzerman; Eddy Sotelo; Gerard J. P. van Westen; Johan Åqvist; Hugo Gutiérrez-de-Terán (PLoS Comput. Biol., 2021)

Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening. - 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 (J. Chem. Inf. Model., 2022)

Papyrus: a large-scale curated dataset aimed at bioactivity predictions. - Olivier J. M. Béquignon; Brandon J. Bongers; Willem Jespers; Adriaan P. IJzerman; B. van der Water; Gerard J. P. van Westen (J. Cheminformatics, 2023)

Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. - Brandon J. Bongers; Huub J. Sijben; Peter B. R. Hartog; Andrey Tarnovskiy; Adriaan P. IJzerman; Laura H. Heitman; Gerard J. P. van Westen (J. Chem. Inf. Model., 2023)

Large-Scale Modeling of Sparse Protein Kinase Activity Data. - Sohvi Luukkonen; Erik Meijer 004; Giovanni Tricarico; Johan Hofmans; Pieter F. W. Stouten; Gerard J. P. van Westen; Eelke B. Lenselink (J. Chem. Inf. Model., 2023)

DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. - Martin Sícho; Sohvi Luukkonen; Helle W. van den Maagdenberg; Linde Schoenmaker; Olivier J. M. Béquignon; Gerard J. P. van Westen (J. Chem. Inf. Model., 2023)

Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells. - Olivier J. M. Béquignon; Jose C. 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 (J. Chem. Inf. Model., 2023)

3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors. - 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 (J. Cheminformatics, 2023)

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2023)

UnCorrupt SMILES: a novel approach to de novo design. - Linde Schoenmaker; Olivier J. M. Béquignon; Willem Jespers; Gerard J. P. van Westen (J. Cheminformatics, 2023)

AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models. - Andrius Bernatavicius; Martin Sícho; Antonius P. A. Janssen; Alan Kai Hassen; Mike Preuss; Gerard J. P. van Westen (J. Chem. Inf. Model., 2024)

QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool. - 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; et al. (J. Cheminformatics, 2024)

Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design. - 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 (J. Chem. Inf. Model., 2025)

Toward Assay-Aware Bioactivity Model(er)s: Getting a Grip on Biological Context. - Linde Schoenmaker; Enzo G. Sastrokarijo; Laura H. Heitman; Joost B. Beltman; Willem Jespers; Gerard J. P. van Westen (J. Chem. Inf. Model., 2025)

Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design. - 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 (J. Cheminformatics, 2025)