Attachment: publications list
Articles in peer-reviewed journals:
González Hernández, Manuel A., Jennifer Venhorst, Lars Verschuren, Karin Toet, Martien PM Caspers, Martine C. Morrison, Beatrice Coornaert, Gerard JP van Westen, and Roeland Hanemaaijer.
Improved Translational Relevance of In Vitro Fibrosis Models by Integrating IOX2-Mediated Hypoxia-Mimicking Pathways.
Biomedicines 13, no. 6 (2025): 1448. https://doi.org/10.3390/biomedicines13061448
Badr, Nada, Luca Ten Elshof, Ruben D. Houvast, Lysanne DAN de Muynck, A. Crobach, Gerard JP van Westen, Ronald LP van Vlierberghe, J. Sven D. Mieog, Alexander L. Vahrmeijer, and Peter JK Kuppen.
Evaluation of tumor targets selected from public genomic databases for imaging of pancreatic ductal adenocarcinoma.
Scientific Reports 15, no. 1 (2025): 1-12. https://doi.org/10.1038/s41598-025-00517-1
van den Maagdenberg, Helle W., Jikke de Mol van Otterloo, JG Coen van Hasselt, Piet H. van der Graaf, and Gerard JP van Westen.
Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design.
Journal of Chemical Information and Modeling 65, no. 10 (2025): 4783-4796. https://doi.org/10.1021/acs.jcim.5c00107
Meyer, Alina, Bola Khalil, Margarita Iljin, Hester Bange, Leo S. Price, Natalia Dyubankova, Gerard JP van Westen, Herman van Vlijmen, Dorien JM Peters, and Per Artursson.
A Patient-Derived 3D Cyst Model of Polycystic Kidney Disease That Mimics Disease Development and Responds to Repurposing Candidates.
Clinical and Translational Science 18, no. 4 (2025): e70214. https://doi.org/10.1111/cts.70214
Voogd, Linda, Remco L. van den Broek, Marjolein van Wolfswinkel, Kees LMC Franken, Paula Ruibal, Willem Jespers, Judith Leitner et al.
HLA-E/peptide complexes differentially interact with NKG2A/CD94 and T cell receptors.
The Journal of Immunology 214, no. 4 (2025): 595-605. https://doi.org/10.1093/jimmun/vkae068
Hassen, Alan Kai, Martin Šícho, Yorick J. van Aalst, Mirjam CW Huizenga, Darcy NR Reynolds, Sohvi Luukkonen, Andrius Bernatavicius et al.
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design.
Journal of Cheminformatics 17, no. 1 (2025): 41. https://doi.org/10.1186/s13321-024-00910-4
Schoenmaker, Linde, Enzo G. Sastrokarijo, Laura H. Heitman, Joost B. Beltman, Willem Jespers, and Gerard JP van Westen.
Toward Assay-Aware Bioactivity Model (er) s: Getting a Grip on Biological Context.
Journal of Chemical Information and Modeling (2025). https://doi.org/10.1021/acs.jcim.5c00603
Schoenmaker, Linde, Daan A. Jiskoot, Jenke Scheen, Evien Cheng, Vytautas Gapsys, David F. Hahn, Benjamin Ries, Gerard JP van Westen, David L. Mobley, and Willem Jespers.
IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates.
The Journal of Physical Chemistry B 129, no. 9 (2025): 2370-2379. https://doi.org/10.1021/acs.jpcb.4c07156
Gülave, Berfin, Helle W. van den Maagdenberg, Luke van Boven, Gerard JP van Westen, Elizabeth CM de Lange, and JG Coen van Hasselt.
Prediction of the Extent of Blood–Brain Barrier Transport Using Machine Learning and Integration into the LeiCNS-PK3.0 Model.
Pharmaceutical Research 42, no. 2 (2025): 281-289. https://doi.org/10.1007/s11095-025-03828-0
Aslam, Ehsan, Asina Gijasi, Caroline Perner, Rob van Wijk, Anne-Grete Märtson, Gerard JP van Westen, Ilze Bot, Laura H. Heitman, and Alireza Mashaghi.
Immunobiology and pharmacology of neuropeptide substance P.
In Substance P, pp. 625-660. Academic Press, 2025. https://doi.org/10.1016/B978-0-443-22194-1.00001-X
Feng, Chenlin, Rongfang Liu, Reno Brooks, Xuesong Wang, Willem Jespers, Marina Gorostiola González, Gerard JP van Westen, Erik HJ Danen, and Laura H. Heitman.
The effect of cancer-associated mutations on ligand binding and receptor function–A case for the 5-HT2C receptor.
European Journal of Pharmacology 985 (2024): 177081. https://doi.org/10.1016/j.ejphar.2024.177081
van den Maagdenberg, Helle W., Martin Šícho, David Alencar Araripe, Sohvi Luukkonen, Linde Schoenmaker, Michiel Jespers, Olivier JM Béquignon et al.
QSPRpred: a flexible open-source quantitative structure-property relationship modelling tool.
Journal of Cheminformatics 16, no. 1 (2024): 128. https://doi.org/10.1186/s13321-024-00908-y
Bernatavicius, Andrius, Martin Šícho, Antonius PA Janssen, Alan Kai Hassen, Mike Preuss, and Gerard JP van Westen.
AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models.
Journal of Chemical Information and Modeling 64, no. 21 (2024): 8113-8122. https://doi.org/10.1021/acs.jcim.4c00309
van den Broek, Remco L., Xabier Bello, Rebecca V. Küpper, Gerard JP van Westen, Willem Jespers, and Hugo Gutiérrez-de-Terán.
Memprot. GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell.
Bioinformatics 40, no. 11 (2024): btae662. https://doi.org/10.1093/bioinformatics/btae662
González Hernández, Manuel A., Lars Verschuren, Martien PM Caspers, Martine C. Morrison, Jennifer Venhorst, Jelle T. van den Berg, Beatrice Coornaert, Roeland Hanemaaijer, and Gerard JP van Westen.
Identifying patient subgroups in MASLD and MASH-associated fibrosis: molecular profiles and implications for drug development.
Scientific Reports 14, no. 1 (2024): 23362. https://doi.org/10.1038/s41598-024-74098-w
den Hollander, Lisa S., Annelien JM Zweemer, Olivier JM Béquignon, Dora M. Hammerl, Bente TM Bleijs, Margo Veenhuizen, Wernard JF Lantsheer et al.
CC chemokine receptor 2 is allosterically modulated by sodium ions and amiloride derivatives through a distinct sodium ion binding site.
Biochemical Pharmacology (2024): 116464. https://doi.org/10.1016/j.bcp.2024.116464
Beerkens, Bert LH, Vasiliki Andrianopoulou, Xuesong Wang, Rongfang Liu, Gerard JP van Westen, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, and Daan van der Es.
N-Acyl-N-Alkyl Sulfonamide Probes for Ligand-Directed Covalent Labeling of GPCRs: The Adenosine A2B Receptor as Case Study.
ACS Chemical Biology 19, no. 7 (2024): 1554-1562. https://doi.org/10.1021/acschembio.4c00210
Dilweg, Majlen A., Marina Gorostiola González, Martijn D. de Ruiter, Nadine J. Meijboom, Jacobus PD van Veldhoven, Rongfang Liu, Willem Jespers et al.
Exploring novel dilazep derivatives as hENT1 inhibitors and potentially covalent molecular tools.
Purinergic Signalling (2024): 1-28. https://doi.org/10.1007/s11302-024-10026-x
Gorostiola González, Marina, Pepijn RJ Rakers, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, and Gerard JP van Westen.
Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities.
International Journal of Molecular Sciences 25, no. 7 (2024): 3698. https://doi.org/10.3390/ijms25073698
van Veggel, Lieve, Tamara AM Mocking, Hubert J. Sijben, Rongfang Liu, Marina Gorostiola González, Majlen A. Dilweg, Jeroen Royakkers et al.
Still in Search for an EAAT Activator: GT949 Does Not Activate EAAT2, nor EAAT3 in Impedance and Radioligand Uptake Assays.
ACS Chemical Neuroscience 15, no. 7 (2024): 1424-1431. https://doi.org/10.1021/acschemneuro.3c00731
Houvast, Ruben D., Nada Badr, Taryn March, Lysanne DAN de Muynck, Vincent Q. Sier, Timo Schomann, Shadhvi Bhairosingh et al.
Preclinical evaluation of EpCAM-binding designed ankyrin repeat proteins (DARPins) as targeting moieties for bimodal near-infrared fluorescence and photoacoustic imaging of cancer.
European Journal of Nuclear Medicine and Molecular Imaging 51, no. 8 (2024): 2179-2192. https://doi.org/10.1007/s00259-023-06407-w
Gorostiola González, Marina, Hubert J. Sijben, Laura Dall’Acqua, Rongfang Liu, Adriaan P. IJzerman, Laura H. Heitman, and Gerard JP van Westen.
Molecular insights into disease-associated glutamate transporter (EAAT1/SLC1A3) variants using in silico and in vitro approaches.
Frontiers in Molecular Biosciences 10 (2023): 1286673. https://doi.org/10.3389/fmolb.2023.1286673
Mullowney, Michael W., Katherine R. Duncan, Somayah S. Elsayed, Neha Garg, Justin JJ van der Hooft, Nathaniel I. Martin, David Meijer et al.
Artificial intelligence for natural product drug discovery.
Nature Reviews Drug Discovery 22, no. 11 (2023): 895-916. https://doi.org/10.1038/s41573-023-00774-7
Béquignon, Olivier JM, Jose C. Gómez-Tamayo, Eelke B. Lenselink, Steven Wink, Steven Hiemstra, Chi Chung Lam, Domenico Gadaleta et al.
Collaborative SAR modeling and prospective in vitro validation of oxidative stress activation in human HepG2 cells.
Journal of chemical information and modeling 63, no. 17 (2023): 5433-5445. https://doi.org/10.1021/acs.jcim.3c00220
Gorostiola González, Marina, Remco L. van den Broek, Thomas GM Braun, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, and Gerard JP van Westen.
3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors.
Journal of Cheminformatics 15, no. 1 (2023): 74. https://doi.org/10.1186/s13321-023-00745-5
Sicho, Martin, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier JM Béquignon, and Gerard JP van Westen.
DrugEx: deep learning models and tools for exploration of drug-like chemical space.
Journal of chemical information and modeling 63, no. 12 (2023): 3629-3636. https://doi.org/10.1021/acs.jcim.3c00434
Luukkonen, Sohvi, Erik Meijer, Giovanni A. Tricarico, Johan Hofmans, Pieter FW Stouten, Gerard JP van Westen, and Eelke B. Lenselink.
Large-scale modeling of sparse protein kinase activity data.
Journal of Chemical Information and Modeling 63, no. 12 (2023): 3688-3696. https://doi.org/10.1021/acs.jcim.3c00132
Beerkens, Bert LH, Inge M. Snijders, Joep Snoeck, Rongfang Liu, Anton TJ Tool, Sylvia E. Le Dévédec, Willem Jespers et al.
Development of an Affinity-Based Probe to Profile Endogenous Human Adenosine A3 Receptor Expression.
Journal of Medicinal Chemistry 66, no. 16 (2023): 11399-11413. https://doi.org/10.1021/acs.jmedchem.3c00854
Bournez, Colin, Martijn Riool, Leonie de Boer, Robert A. Cordfunke, Leonie de Best, Remko van Leeuwen, Jan Wouter Drijfhout, Sebastian AJ Zaat, and Gerard JP van Westen.
CalcAMP: a new machine learning model for the accurate prediction of antimicrobial activity of peptides.
Antibiotics 12, no. 4 (2023): 725. https://doi.org/10.3390/antibiotics12040725
Bongers, Brandon J., Huub J. Sijben, Peter BR Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, and Gerard JP van Westen.
Proteochemometric modeling identifies chemically diverse norepinephrine transporter inhibitors.
Journal of Chemical Information and Modeling 63, no. 6 (2023): 1745-1755. https://doi.org/10.1021/acs.jcim.2c01645
Schoenmaker, Linde, Olivier JM Béquignon, Willem Jespers, and Gerard JP van Westen.
UnCorrupt SMILES: a novel approach to de novo design.
Journal of Cheminformatics 15, no. 1 (2023): 22. https://doi.org/10.1186/s13321-023-00696-x
Liu, Xuhan, Kai Ye, Herman WT van Vlijmen, Adriaan P IJzerman, and Gerard jp van Westen.
DrugEx v3: Scaffold-Constrained Drug Design with Graph Transformer-based Reinforcement Learning.
Journal of Cheminformatics 15, no. 1 (2023): 24. https://doi.org/10.1186/s13321-023-00694-z
Luukkonen, Sohvi , Helle W. van den Maagdenberg, Michael T. M. Emmerich and Gerard JP van Westen.
Artificial intelligence in multi-objective drug design.
Current Opinion in Structural Biology 79 (2023): 102537. https://doi.org/10.1016/j.sbi.2023.102537
den Hollander, Lisa S., Olivier JM Béquignon, Xuesong Wang, Kim van Wezel, Jeremy Broekhuis, M. Gorostiola González, Karin E. de Visser, Adriaan P. IJzerman, Gerard JP van Westen, and Laura H. Heitman.
Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism.
Biochemical Pharmacology 208 (2023): 115399. https://doi.org/10.1016/j.bcp.2022.115399
Béquignon, Olivier JM, Brandon J. Bongers, Willem Jespers, Ad P. IJzerman, B. van der Water, and Gerard JP van Westen.
Papyrus: a large-scale curated dataset aimed at bioactivity predictions.
Journal of Cheminformatics 15, no. 1 (2023): 3. https://doi.org/10.1186/s13321-022-00672-x
van der Wall, H. E. C., R. J. Doll, Gerard JP van Westen, T. Niemeyer-van der Kolk, G. Feiss, H. Pinckaers, M. B. A. van Doorn et al.
Discriminative Machine Learning Analysis for Skin Microbiome: Observing Biomarkers in Patients with Seborrheic Dermatitis.
Journal of Artificial Intelligence for Medical Sciences 3, no. 1-2 (2022): 1-7. http://dx.doi.org/10.55578/joaims.220819.001
Feng, Chenlin, Xuesong Wang, Willem Jespers, Rongfang Liu, Sofía Denise Zamarbide Losada, Marina Gorostiola González, Gerard JP van Westen, Erik HJ Danen, and Laura H. Heitman.
Cancer-associated mutations of the adenosine A2A receptor have diverse influences on ligand binding and receptor functions.
Molecules 27, no. 15 (2022): 4676. https://doi.org/10.3390/molecules27154676
van Zwol, Willemien, Antoine Rimbert, Justina C. Wolters, Marieke Smit, Vincent W. Bloks, Niels J. Kloosterhuis, Nicolette CA Huijkman, Gerard JP van Westen, et al.
Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion.
Hepatology (2022). https://doi.org/10.1002/hep.32709
Hassing, Gerardus J., Michiel J. van Esdonk, Gerard JP van Westen, Adam F. Cohen, Jacobus Burggraaf, and Pim Gal.
Dose escalations in phase I studies: Feasibility of interpreting blinded pharmacodynamic data.
British Journal of Clinical Pharmacology 88, no. 12 (2022): 5412-5419. https://doi.org/10.1111/bcp.15473
Liu, Qiuyu, Wanda van der Stel, Vera E. van der Noord, Hanneke Leegwater, Bircan Coban, Kim Elbertse, Joannes TM Pruijs, Gerard JP van Westen, et al.
Hypoxia triggers TAZ phosphorylation in basal a triple negative breast cancer cells.
International Journal of Molecular Sciences 23, no. 17 (2022): 10119. https://doi.org/10.3390/ijms231710119
Bongers, B. J., M. Gorostiola González, X. Wang, H. W. T. van Vlijmen, W. Jespers, H. Gutiérrez-de-Terán, K. Ye, A. P. IJzerman, L. H. Heitman, and Gerard JP van Westen.
Pan-cancer functional analysis of somatic mutations in G protein-coupled receptors.
Scientific Reports 12, no. 1 (2022): 21534. https://doi.org/10.1038/s41598-022-25323-x
Wang, Xuesong, Willem Jespers, Just J. de Waal, Kim AN Wolff, L. van Uden, Adriaan P. IJzerman, Gerard JP van Westen, and Laura H. Heitman.
Cancer-related somatic mutations alter adenosine A1 receptor pharmacology: a focus on mutations in the loops and C-terminus.
The FASEB Journal 36, no. 6 (2022). https://doi.org/10.1096/fj.202200203RR
Wang, Xuesong, Willem Jespers, Kim AN Wolff, Jill Buytelaar, Adriaan P. IJzerman, Gerard JP van Westen, and Laura H. Heitman.
Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology.
Molecules 27, no. 12 (2022): 3742. https://doi.org/10.3390/molecules27123742
González, Marina Gorostiola, Antonius PA Janssen, Adriaan P. IJzerman, Laura H. Heitman, and Gerard JP van Westen.
Oncological drug discovery: AI meets structure-based computational research.
Drug discovery today (2022). https://doi.org/10.1016/j.drudis.2022.03.005
Tuerkova, Alzbeta, Brandon J. Bongers, Ulf Norinder, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, Gergely Szakács, Csilla Os zvegy-Laczka, Gerard JP van Westen, and Barbara Zdrazil.
Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening.
Journal of Chemical Information and Modeling (2022). https://doi.org/10.1021/acs.jcim.1c01460
van der Wall, Hein EC, Gert-Jan Hassing, Robert-Jan Doll, Gerard JP van Westen, Adam F. Cohen, Jasper L. Selder, Michiel Kemme, Jacobus Burggraaf, and Pim Gal.
Cardiac age detected by machine learning applied to the surface ECG of healthy subjects: Creation of a benchmark.
Journal of Electrocardiology 72 (2022): 49-55. https://doi.org/10.1016/j.jelectrocard.2022.03.001
Martens, Marvin, Rob Stierum, Emma L. Schymanski, Chris T. Evelo, Reza Aalizadeh, Hristo Aladjov, Kasia Arturi, Gerard JP van Westen, et al.
ELIXIR and Toxicology: a community in development.
F1000Research 10, no. 1129 (2021): 1129. https://doi.org/10.12688/f1000research.74502.1
Amelia, Tasia, Jacobus PD van Veldhoven, Matteo Falsini, Rongfang Liu, Laura H. Heitman, Gerard JP van Westen, Elena Segala et al.
Crystal structure and subsequent ligand design of a nonriboside partial agonist bound to the adenosine A2A receptor.
Journal of Medicinal Chemistry 64, no. 7 (2021): 3827-3842. https://doi.org/10.1021/acs.jmedchem.0c01856
Jespers, Willem, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard JP Van Westen, Johan Åqvist, and Hugo Gutiérrez-de-Terán.
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations.
PLoS Computational Biology 17, no. 11 (2021): e1009152. https://doi.org/10.1371/journal.pcbi.1009152
Liu, Xuhan, Kai Ye, Herman WT van Vlijmen, Michael TM Emmerich, Adriaan P. IJzerman, and Gerard JP van Westen.
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology.
Journal of cheminformatics 13, no. 1 (2021): 85. https://doi.org/10.1186/s13321-021-00561-9
Xiong, Zhaoping, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Gerard JP van Westen, The Multi-Targeting Drug DREAM Challenge Community et al.
Crowdsourced identification of multi-target kinase inhibitors for RET-and TAU-based disease: the Multi-Targeting Drug DREAM Challenge.
PLoS computational biology 17, no. 9 (2021): e1009302. https://doi.org/10.1371/journal.pcbi.1009302
Sicho, Martin, Xuhan Liu, Daniel Svozil, and Gerard JP van Westen.
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics.
Journal of Cheminformatics 13, no. 1 (2021): 1-17. https://doi.org/10.1186/s13321-021-00550-y
Gao, Yongzhi, Matthijs J. Van Haren, Ned Buijs, Paolo Innocenti, Yurui Zhang, Davide Sartini, Roberto Campagna, Gerard JP van Westen et al.
Potent inhibition of nicotinamide N-methyltransferase by alkene-linked bisubstrate mimics bearing electron deficient aromatics.
Journal of Medicinal Chemistry 64, no. 17 (2021): 12938-12963. https://doi.org/10.1021/acs.jmedchem.1c01094
Van der Wall, H. E. C., R. J. Doll, Gerard JP van Westen, I. Koopmans, R. G. Zuiker, J. Burggraaf, and A. F. Cohen.
Using machine learning techniques to characterize sleep-deprived driving behavior.
Traffic injury prevention 22, no. 5 (2021): 366-371. https://doi.org/10.1080/15389588.2021.1914837
Wang, Xuesong, Gerard JP van Westen, Laura H. Heitman, and Adriaan P. IJzerman.
G protein-coupled receptors expressed and studied in yeast. The adenosine receptor as a prime example.
Biochemical Pharmacology 187 (2021): 114370. https://doi.org/10.1016/j.bcp.2020.114370
Wang, Xuesong, Willem Jespers, Rubén Prieto-Díaz, Maria Majellaro, Adriaan P. IJzerman, Gerard JP Van Westen, Eddy Sotelo, Laura H. Heitman, and Hugo Gutiérrez-de-Terán.
Identification of V6. 51L as a selectivity hotspot in stereoselective A2B adenosine receptor antagonist recognition.
Scientific Reports 11, no. 1 (2021): 14171. https://doi.org/10.1038/s41598-021-93419-x
Tehrani, Kamaleddin HME, Nicola Wade, Vida Mashayekhi, Nora C. Brüchle, Willem Jespers, Koen Voskuil, Diego Pesce, Matthijs J. Van Haren, Gerard JP Van Westen, and Nathaniel I. Martin.
Novel cephalosporin conjugates display potent and selective inhibition of imipenemase-type metallo-β-lactamases.
Journal of Medicinal Chemistry 64, no. 13 (2021): 9141-9151. https://doi.org/10.1021/acs.jmedchem.1c00362
Kovacikova, Kristina, Marina Gorostiola González, Rhian Jones, Juan Reguera, Alba Gigante, María-Jesús Pérez-Pérez, Gerhard Pürstinger, Gerard JP van Westen, et al.
Structural insights into the mechanisms of action of functionally distinct classes of chikungunya virus nonstructural protein 1 inhibitors.
Antimicrobial Agents and Chemotherapy 65, no. 7 (2021): e02566-20. https://doi.org/10.1128/AAC.02566-20
Mohr, Florian, Thomas Hurrle, Lindsey Burggraaff, Lukas Langer, Martijn P. Bemelmans, Maximilian Knab, Martin Nieger, Gerard JP van Westen, Laura H. Heitman, and Stefan Bräse.
Synthesis and SAR evaluation of coumarin derivatives as potent cannabinoid receptor agonists.
European Journal of Medicinal Chemistry 220 (2021): 113354. https://doi.org/10.1016/j.ejmech.2021.113354
Leeuwen, T. van, C. Araman, L. P. Pournara, A. S. B. Kampstra, T. Bakkum, M. H. S. Marqvorsen, C. R. Nascimento, Gerard JP van Westen et al.
Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens.
RSC Chemical Biology 2, no. 3 (2021): 855-862. https://doi.org/10.1039/D1CB00009H
Wang, Xuesong, Gerard JP van Westen, Laura H. Heitman, and Adriaan P. IJzerman.
G protein-coupled receptors expressed and studied in yeast. The adenosine receptor as a prime example.
Biochemical Pharmacology 187 (2021): 114370. https://doi.org/10.1016/j.bcp.2020.114370
Van der Wall, H. E. C., R. J. Doll, Gerard JP van Westen, I. Koopmans, R. G. Zuiker, J. Burggraaf, and A. F. Cohen.
Using machine learning techniques to characterize sleep-deprived driving behavior.
Traffic injury prevention 22, no. 5 (2021): 366-371. https://doi.org/10.1080/15389588.2021.1914837
Fienieg, Bart, Gerardus J. Hassing, Hein EC van der Wall, Gerard JP van Westen, Michiel JB Kemme, Ahmet Adiyaman, Arif Elvan, Jacobus Burggraaf, and Pim Gal.
The association between body temperature and electrocardiographic parameters in normothermic healthy volunteers.
Pacing and Clinical Electrophysiology 44, no. 1 (2021): 44-53. https://doi.org/10.1111/pace.14120
Burggraaff, Lindsey, Amber van Veen, Chi Chung Lam, Herman WT van Vlijmen, Adriaan P. IJzerman, and Gerard JP van Westen.
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs.
Journal of Chemical Information and Modeling 60, no. 10 (2020): 4664-4672. https://doi.org/10.1021/acs.jcim.0c00695
Zhou, Juan, Elliot D. Mock, Karol Al Ayed, Xinyu Di, Vasudev Kantae, Lindsey Burggraaff, Anna F. Stevens, Gerard JP van Westen et al.
Structure–activity relationship studies of α-ketoamides as inhibitors of the phospholipase A and acyltransferase enzyme family.
Journal of Medicinal Chemistry 63, no. 17 (2020): 9340-9359. https://doi.org/10.1021/acs.jmedchem.0c00522
van der Wel, Tom, Riet Hilhorst, Hans den Dulk, Tim van den Hooven, Nienke M. Prins, Joost APM Wijnakker, Bogdan I. Florea, Gerard JP van Westen et al.
Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis.
Nature Communications 11, no. 1 (2020): 3216. https://doi.org/10.1038/s41467-020-17027-5
Škuta, C., Isidro Cortés-Ciriano, Wim Dehaen, P. Kříž, Gerard JP van Westen, Igor V. Tetko, Andreas Bender, and Daniel Svozil.
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping.
Journal of Cheminformatics 12, no. 1 (2020): 1-16. https://doi.org/10.1186/s13321-020-00443-6
Lindsey, Burggraaff, W. T. van Vlijmen Herman, Adriaan P. IJzerman, and Gerard J P van Westen.
Quantitative prediction of selectivity between the A 1 and A 2A adenosine receptors.
Journal of Cheminformatics 12, no. 1 (2020). https://doi.org/10.1186/s13321-020-00438-3
Burggraaff, Lindsey, Eelke B. Lenselink, Willem Jespers, Jesper van Engelen, Brandon J. Bongers, Marina Gorostiola González, Rongfang Liu et al., Gerard JP van Westen.
Successive statistical and structure-based modeling to identify chemically novel kinase inhibitors.
Journal of Chemical Information and Modeling 60, no. 9 (2020): 4283-4295. https://doi.org/10.1021/acs.jcim.9b01204
Qin, Tian, Samantha Prins, Geert Jan Groeneveld, Gerard JP Van Westen, Helga E. de Vries, Yin Cheong Wong, Luc JM Bischoff, and Elizabeth CM de Lange.
Utility of animal models to understand human Alzheimer’s disease, using the mastermind research approach to avoid unnecessary further sacrifices of animals.
International journal of molecular sciences 21, no. 9 (2020): 3158. https://doi.org/10.3390/ijms21093158
Wang, Xuesong, Willem Jespers, Brandon J. Bongers, Maria CC Habben Jansen, Chantal M. Stangenberger, Majlen A. Dilweg, Hugo Gutiérrez-de-Terán, Adriaan P. IJzerman, Laura H. Heitman, and Gerard JP van Westen.
Characterization of cancer-related somatic mutations in the adenosine A2B receptor.
European Journal of Pharmacology 880 (2020): 173126. https://doi.org/10.1016/j.ejphar.2020.173126
Superti-Furga, Giulio, Daniel Lackner, Tabea Wiedmer, Alvaro Ingles-Prieto, Barbara Barbosa, Enrico Girardi, Ulrich Goldmann Gerard JP van Westen et al.
The RESOLUTE consortium: unlocking SLC transporters for drug discovery.
Nature reviews Drug discovery 19, no. 7 (2020): 429-430. https://doi.org/10.1038/d41573-020-00056-6
Malas, Tareq B., Wouter N. Leonhard, Hester Bange, Zoraide Granchi, Kristina M. Hettne, Gerard JP Van Westen, Leo S. Price, Peter AC't Hoen, and Dorien JM Peters.
Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles.
EBioMedicine 51 (2020): 102585. https://doi.org/10.1016/j.ebiom.2019.11.046
Koenders, Sebastiaan TA, Lukas S. Wijaya, Martje N. Erkelens, Alexander T. Bakker, Vera E. van der Noord, Eva J. van Rooden, Lindsey Burggraaff, Gerard JP van Westen et al.
Development of a retinal-based probe for the profiling of retinaldehyde dehydrogenases in cancer cells.
ACS Central Science 5, no. 12 (2019): 1965-1974. https://doi.org/10.1021/acscentsci.9b01022
Ruano-Ordás, David, Lindsey Burggraaff, Rongfang Liu, Cas van der Horst, Laura H. Heitman, Michael TM Emmerich, Jose R. Mendez, Iryna Yevseyeva, and Gerard JP van Westen.
A multiple classifier system identifies novel cannabinoid CB2 receptor ligands.
Journal of Cheminformatics 11 (2019): 1-14. https://doi.org/10.1186/s13321-019-0389-9
Hassing, Gerardus J., Hein EC van der Wall, Gerard JP van Westen, Michiel JB Kemme, Ahmet Adiyaman, Arif Elvan, Jacobus Burggraaf, and Pim Gal.
Blood pressure-related electrocardiographic findings in healthy young individuals.
Blood Pressure 29, no. 2 (2020): 113-122. https://doi.org/10.1080/08037051.2019.1673149
Antonius P.A. Janssen, Jacob M.A. van Hengst, Olivier J.M. Béquignon, Hui Deng, Gerard J.P. van Westen, Mario van der Stelt.
Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors.
J. Med Chem. (2019). https://doi.org/10.1021/acs.jmedchem.9b00686
Dharjath S. Hameed, Aysegul Sapmaz, Lindsey Burggraaff, Alessia Amore, Cornelis J. Slingerland, Gerard J. P. van Westen, Huib Ovaa.
Development of Ubiquitin-Based Probe for Metalloprotease Deubiquitinases.
Angew Chem Int Ed Engl. (2019). https://doi.org/10.1002/anie.201906790
Jichao He, Ronan P. McLaughlin, Vera van der Noord, John A. Foekens, John W. M. Martens, Gerard J.P. van Westen, Yinghui Zhang, Bob van de Water.
Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer.
Breast Cancer Res. Ther. (2019). https://doi.org/10.1007/s10549-019-05380-z
Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, AstraZeneca-Sanger Drug Combination DREAM Consortium, Gerard JP van Westen et al.
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Nature Comm., 10 (1) (2019). https://doi.org/10.1038/s41467-019-09799-2
Paul Oranje, Robin Gouka, Lindsey Burggraaff, Mario Vermeer, Clément Chalet, Guus Duchateau, Pieter van der Pijl, Marian Geldof, Niels de Roo, Fenja Clauwaert, Toon van Paeschen, Johan Nicolaï, Tom de Bruyn, Pieter Annaert, Adriaan P. IJzerman, and Gerard J.P. van Westen.
Novel Natural and Synthetic Inhibitors of Solute Carriers SGLT1 and SGLT2.
Pharmacol Res Perspect. (2019). https://doi.org/10.1002/prp2.504
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Gerard J. P. van Westen.
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor.
J. Cheminf, 11 (2019). https://doi.org/10.1007/s12471-019-1282-x
Gert Jan Hassing, Hein E. C. van der Wall, Gerard J. P. van Westen, Michiel J. B. Kemme, Ahmet Adiyaman, Arif Elvan, Koos Burggraaf, Pim Gal.
Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index.
Neth. Heart J. (2019). https://doi.org/10.1007/s12471-019-1282-x
Tijmen H. Booij, Wouter N. Leonhard, Hester Bange, Kuan Yan, Michiel Fokkelman, Anna J. Plugge, Kimberley A.M. Veraar, Johannes G. Dauwerse, Gerard J.P. van Westen, Bob van de Water, Leo S. Price, and Dorien J. M. Peters.
In vitro 3d phenotypic drug screen identifies celastrol as an effective in vivo inhibitor of polycystic kidney disease.
J. Mol. Cell. Biol. (2019). https://doi.org/10.1093/jmcb/mjz029
Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Gerard J.P. van Westen.
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.
Journal of Cheminformatics 11 (15) (2019). https://doi.org/10.1186/s13321-019-0337-8
Sydow, Dominique, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, and Andrea Volkamer.
Advances and Challenges in Computational Target Prediction.
JCIM, 59 (5) (2019). https://doi.org/10.1021/acs.jcim.8b00832
van der Wall, Hein Evert Christiaan, Pim Gal, Michiel J. B. Kemme, Gerard.J.P. van Westen, and Koos Burggraaf.
Number of ECG Replicates and QT Correction Formula Influences the Estimated QT Prolonging Effect of a Drug.
J. Cardiovasc. Pharmacol., 73 (4) (2019). https://doi.org/10.1097/FJC.0000000000000657
Grimm, Sebastian H., Berend Gagestein, Jordi F. Keijzer, Nora Liu, Ruud H. Wijdeven, Eelke B. Lenselink, Adriaan W. Tuind, Adrianus M.C.H. van den Nieuwendijk, Gerard J.P. van Westen, Constant A.A. van Boeckel, Herman S. Overkleeft, Jacques Neefjes, and Mario van der Stelt.
Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors.
Bioorg. & med. Chem., 27 (5) (2019). https://doi.org/10.1016/j.bmc.2019.01.006
Zhou, Juan, Elliot D. Mock, Andrea Martella, Vasudev Kantae, Xinyu Di, Lindsey Burggraaff, Marc P. Baggelaar, Karol Al-Ayed, Alexander Bakker, Bogdan I. Florea, Sebastian H. Grimm, Hans den Dulk, Chun T. Li, Laura Mulder, Herman S. Overkleeft, Thomas Hankemeier, Gerard J. P. van Westen, and Mario van der Stelt.
Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI.
Acs Chem. Biol. 14 (2) (2019). https://doi.org/10.1021/acschembio.8b00969
Miggiels, Paul, Bert Wouters, Gerard J.P. van Westen, Anne-Charlotte Dubbelman, and Thomas Hankemeier.
Novel technologies for metabolomics: More for less.
TrAC (2019). https://doi.org/10.1016/j.trac.2018.11.021
Janssen, Antonius P. A., Sebastian H. Grimm, Ruud H. M. Wijdeven, Eelke B. Lenselink, Jacques Neefjes, Constant A. A. van Boeckel, Gerard J. P. van Westen, and Mario van der Stelt.
Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome–Inhibitor Interaction Landscapes.
JCIM, 53 (3) (2019). https://doi.org/10.1021/acs.jcim.8b00640
Yang, Mi, Jaak Simm, Chi Chung Lam, Pooya Zakeri, Gerard JP van Westen, Yves Moreau, and Julio Saez-Rodriguez.
Linking drug target and pathway activation for effective therapy using multi-task learning.
Nature Scientific Reports, 8 (2018). https://doi.org/10.1038/s41598-018-25947-y
Jespers, Willem, Anke C. Schiedel, Laura H. Heitman, Robert M. Cooke, Lisa Kleene, Gerard J. P. van Westen, David E. Gloriam, Christa E. Müller, Eddy Sotelo, and Hugo Gutiérrez-de-Terán.
Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms.
TiPS, 39 (1) (2018). https://dx.doi.org/10.1016/j.tips.2017.11.001
Vlot, Anna H. C., Wilhelmus E. A. de Witte, Meindert Danhof, Piet H. van der Graaf, Gerard J. P. van Westen, and Elizabeth C. M. de Lange.
Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure-Activity Modeling.
The AAPS Journal, 20 (11) (2018). https://doi.org/10.1208/s12248-017-0172-7
Tresadern, Gary, Andres A. Trabanco, Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, and Gerard J. P. van Westen.
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.
JCIM, 57 (12) (2018). https://doi.org/10.1021/acs.jcim.7b00338
Donkers, Joanne M., Benno Zehnder, Gerard J. P. van Westen, Mark J. Kwakkenbos, Adriaan P. IJzerman, Ronald P. J. Oude Elferink, Ulrich Beuers, Stephan Urban, and Stan F. J. van de Graaf.
Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP.
Nature Scientific Reports, 7 (2017). https://10.1038/s41598-017-15338-0
Lenselink, Eelke B., Niels ten Dijke, Brandon Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, and Gerard J. P. van Westen.
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.
J Cheminf. 9 (45) (2017). https://doi.org/10.1186/s13321-017-0232-0
Booij, Tijmen H., Hester Bange, Wouter N. Leonhard, Kuan Yan, Michiel Fokkelman, Steven J. Kunnen, Johannes G. Dauwerse, Yu Qin, Bob van de Water, Gerard J.P. van Westen, Dorien J.M. Peters, and Leo S. Price.
High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease.
SLAS Discovery, 28 (8) (2017): 974-984. https://doi.org/10.1177/2472555217716056
Paricharak, Shardul, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, and Gerard J. P. van Westen.
Data-driven approaches used for compound library design, hit triage, and bioactivity modeling in high-throughput screening.
Brief. Bioinform. (2016). https://doi.org/10.1093/bib/bbw105
Lenselink, Eelke B., Willem Jespers, Herman W.T. Van Vlijmen, Adriaan P. IJzerman, and Gerard J.P. van Westen.
Interacting with GPCRs; on the use of Interaction Fingerprints for Virtual Screening.
JCIM (2016). https://doi.org/10.1021/acs.jcim.6b00314
Christmann-Franck, Serge, Gerard J.P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, and Daniel Domine.
Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound–Kinase Activities: A Way toward Selective Promiscuity by Design?
JCIM, 56 (9) (2016): 1654-1675. https://doi.org/10.1021/acs.jcim.6b00122
Cortés-Ciriano, Isidro, Gerard J.P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, and Thérèse E. Malliavin.
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.
Bioinformatics, 32(1) (2015): 85-95. https://doi.org/10.1093/bioinformatics/btv529
Murrell, Daniel S., Isidro Cortes-Ciriano, Gerard J.P. van Westen, Ian Stott, Andreas Bender, Therese E. Malliavin, and Robert C. Glen.
Chemically Aware Model Builder (camb): An R package for property and bioactivity modelling of small molecules.
J. Cheminf., 7 (2015). https://doi.org/10.1186/s13321-015-0086-2
Gaulton, Anna, Namrata Kale, Gerard J.P. van Westen, Louisa J. Bellis, A. Patrícia Bento, Mark Davies, Anne Hersey, George Papadatos, Mark Forster, Philip Wege, and John P. Overington.
A large-scale crop protection bioassay data set.
Scientific Data 2, 150032 (2015). https://doi.org/10.1038/sdata.2015.32
Mugumbate, Grace, Katherine A. Abrahams, Jonathan A.G. Cox, George Papadatos, Gerard J.P. van Westen, Joel Lelievre, Szymon T. Calus, Nick Loman, Lluis Ballell, David Barros, John P. Overington, and Gurdyal S. Besra.
Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation.
PLoS ONE, 10(3) (2015): e0121492. https://doi.org/10.1371/journal.pone.0121492
Li, P., D. Rial, P. M Canas, J-H Yoo, W. Li, X Zhou, Y. Wang, Gerard J.P. van Westen, M-P Payen, E. Augusto, N. Gonçalves, A. R. Tomé, Z. Li, Z. Wu, X. Hou, Y. Zhou, Adriaan P. IJzerman, E. S. Boyden, R. A. Cunha, J. Qu, and J-F Chen.
Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory.
Mol. Psychiatry, 20 (2015). https://doi.org/10.1038/mp.2014.182
Bansal, Mukesh, Jichen Yang, Charles Karan, Michael P. Menden, James C. Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura M. Heiser, Ronald Realubit, Michela Mattioli, Mariano J. Alvarez, Yao Shen, NCI-DREAM Community, Gerard J.P. van Westen, Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky, and Andrea Califano.
A community computational challenge to predict the activity of pairs of compounds.
Nature Biotech, 32 (2014). https://doi.org/10.1038/nbt.3052
Cortes-Ciriano, Isidro, Daniel S. Murrell, Gerard J.P. van Westen, Andreas Bender, and Thérèse E. Malliavin.
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modelling.
J. Cheminf, 7 (2015). https://doi.org/10.1186/s13321-014-0049-z
Cortes-Ciriano, Isidro, Qurrat U. Ain, Vigneshwari Subramanian, Eelke B. Lenselink, Oscar Mendez-Lucio, Adriaan P. IJzerman, Gerd Wohlfahrt, Peteris Prusis, Thérèse E. Malliavin, Gerard J.P. van Westen, and Andreas Bender.
Polypharmacology Modelling Using Proteochemometrics (PCM): Recent Methodological Developments, Applications to Target Families, and Future Prospects.
MedChemComm, 6 (2015). https://doi.org/10.1039/C4MD00216D
Davies, Mark, Michał Nowotka, George Papadatos, Francis Atkinson, Gerard J.P. van Westen, Nathan Dedman, Rodrigo Ochoa, and John P. Overington.
MyChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data.
Challenges, 5 (2014). https://doi.org/10.3390/challe5020334
Ain, Qurrat U., Oscar Méndez-Lucio, Isidro Cortés Ciriano, Thérèse Malliavin, Gerard JP van Westen, and Andreas Bender.
Modelling ligand selectivity of Serine Proteases using integrative Proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features.
Integrative Biology 6 (2014): 1023-1033. https://doi.org/10.1039/C4IB00175C
Peeters, Miriam C., Qilan Li, Rachel Elands, Gerard J.P. van Westen, Eelke B. Lenselink, Christa E. Müller, and Adriaan P. IJzerman.
Domains for activation and inactivation in G protein-coupled receptors–a mutational analysis of constitutive activity of the adenosine A2B receptor.
Biochemical Pharmacology 92 (2014): 348–357. https://doi.org/10.1016/j.bcp.2014.08.022
Lebedev, Alexander V., Eric Westman, Gerard J.P. Van Westen, Milica G. Kramberger, Arvid Lundervold, Dag Aarsland, Hillka Soininen, Iwona Kłoszewska, Patrizia Mecocci, Magda Tsolaki, Bruno Vellas, Simon Lovestone, and Andy Simmons.
Random Forest ensembles for detection and prediction of Alzheimer's Disease with a good between-cohort robustness.
Neuroimage: Clinical 6 (2014): 115-125. https://doi.org/10.1016/j.nicl.2014.08.023
Papadatos, George, Gerard J.P. van Westen, Samuel Croset, Rita Santos, Simone Trubian, and John P. Overington.
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus.
Journal of Cheminformatics 6 (2014): 40. https://doi.org/10.1186/s13321-014-0040-8
Kufareva, Irina, Vsevolod Katritch, Participants of GPCR Dock2013, Gerard J.P. van Westen, Raymond C. Stevens, and Ruben Abagyan.
Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges.
Structure 22 (2014): 1120-1139. https://doi.org/10.1016/j.str.2014.06.012
Cortes-Ciriano, Isidro, Gerard J.P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, and Thérèse Malliavin.
Proteochemometric modeling in a Bayesian framework.
Journal of Cheminformatics 6 (2014): 35. https://doi.org/10.1186/1758-2946-6-35
Costello, James C., Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P. Menden, Nicholas J. Wang, Mukesh Bansal, ... Gerard JP Van Westen, ... and NCI DREAM Community.
A community effort to assess and improve drug sensitivity prediction algorithms.
Nature Biotechnology 32 (2014): 1202-1212. https://doi.org/10.1038/nbt.2877
Gerard J.P. van Westen, Andreas Bender, and John P. Overington.
Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modeling.
Journal of Chemical Biology 7 (2014): 119-123. https://doi.org/10.1007/s12154-014-0112-2
Gerard J.P. van Westen, Anna Gaulton, and John P. Overington.
Chemical, Target, and Bioactive Properties of Allosteric Modulation.
PLoS Computational Biology 10 (2014): e1003559. https://doi.org/10.1371/journal.pcbi.1003559
Gerard J.P. van Westen, Remco F. Swier, Isidro Cortes-Ciriano, Jörg K. Wegner, John P. Overington, Adriaan P. IJzerman, Herman WT van Vlijmen, and Andreas Bender.
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
Journal of Cheminformatics 5 (2013): 42. https://doi.org/10.1186/1758-2946-5-42
Gerard J.P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman WT van Vlijmen, and Andreas Bender.
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets.
Journal of Cheminformatics 5 (2013): 41. https://doi.org/10.1186/1758-2946-5-41
De Bruyn, Tom, Gerard J.P. van Westen, Adriaan P. IJzerman, Bruno Stieger, Peter de Witte, Patrick F. Augustijns, and Pieter P. Annaert.
Structure-based identification of OATP1B1/3 inhibitors.
Molecular Pharmacology 83 (2013): 1257-1267. https://doi.org/10.1124/mol.112.084152
Gerard J.P. van Westen and John P. Overington.
A ligand’s-eye view of protein similarity.
Nature Methods 10 (2013): 116-117. https://doi.org/10.1038/nmeth.2339
Gerard J.P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W.T. van Vlijmen, and Andreas Bender.
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data.
PLoS Computational Biology 9 (2013): e1002899. https://doi.org/10.1371/journal.pcbi.1002899
Gerard J.P. van Westen, Olaf O. van den Hoven, Rianne van der Pijl, Thea Mulder-Krieger, Henk de Vries, Jörg K. Wegner, Adriaan P. IJzerman, Herman W.T. Van Vlijmen, and Andreas Bender.
Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data.
Journal of Medicinal Chemistry 55 (2012): 7010-7020. https://doi.org/10.1021/jm3003069
Lane, Robert, Carmen Klein Herenbrink, Gerard J.P. van Westen, Jelle A. Spoorendonk, Carsten Hoffman, and Adriaan P. IJzerman.
A Novel Non-ribose Agonist, LUF5834, Engages Distinct Residues from that of Adenosine-like Ligands to Activate the Adenosine A2A Receptor.
Molecular Pharmacology 81 (2012): 475-487. https://doi.org/10.1124/mol.111.075937
Gerard J.P. van Westen, Jörg K. Wegner, Peggy Geluykens, Leen Kwanten, Inge Vereycken, Anik Peeters, Adriaan P. IJzerman, Herman W.T. van Vlijmen, and Andreas Bender.
Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development.
PLoS ONE 6 (2012): e27518. https://doi.org/10.1371/journal.pone.0027518
Peeters, Miriam C., Qilan Li, Gerard J.P. van Westen, and Adriaan P. IJzerman.
Three “hotspots” important for adenosine A2B receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop.
Purinergic Signalling 8 (2011): 23-38. https://doi.org/10.1007/s11302-011-9251-x
Peeters, Miriam C., Gerard J.P. van Westen, Dong Guo, Lisanne E. Wisse, Christa E. Müller, Margot W. Beukers, and Adriaan P. IJzerman.
GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor.
FASEB Journal 25 (2011): 632-643. https://doi.org/10.1096/fj.10-164319
Peeters, Miriam C., Gerard J.P. van Westen, Qilan Li, and Adriaan P. Ijzerman.
The importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation.
Trends in Pharmacological Sciences 32 (2011): 35-42. https://doi.org/10.1016/j.tips.2010.10.001
Gerard J.P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, and Andreas Bender.
Proteochemometric Modeling as a Tool to Design Selective Compounds and for Extrapolating to Novel Targets.
MedChemComm 2 (2011): 16-30. https://doi.org/10.1039/C0MD00165A
van der Horst, Eelke, Julio E. Peironcely, Gerard J.P. van Westen, Olaf O. van den Hoven, Warren R. J. D. Galloway, David R. Spring, Joerg K. Wegner, Herman W. T. van Vlijmen, Ad P. IJzerman, John P. Overington, and Andreas Bender.
Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space.
Current Topics in Medicinal Chemistry 11 (2011): 1964-1977. https://doi.org/10.2174/156802611796391230
Gerard J.P. van Westen, Jörg K. Wegner, Andreas Bender, Adriaan P. IJzerman, and Herman W. T. van Vlijmen.
Mining protein dynamics from sets of crystal structures using "consensus structures".
Protein Science 19 (2010): 742-752. https://doi.org/10.1002/pro.350
Doddareddy, Munikumar R., Gerard J.P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. Ijzerman, Michael Emmerich, Jeremy L. Jenkins, and Andreas Bender.
Chemogenomics: Looking at biology through the lens of chemistry.
Statistical Analysis and Data Mining 2 (2009): 149-160. https://doi.org/10.1002/sam.10046
Book Chapters:
Wang, Xuesong, Gerard JP van Westen, Adriaan P. IJzerman, and Laura H. Heitman.
G Protein-Coupled Receptors and Their Mutations in Cancer–A Focus on Adenosine Receptors.
In GPCRs as therapeutic targets, pp. 631-676. Wiley, 2022. https://doi.org/10.1002/9781119564782.ch18
Béquignon, Olivier JM, Gopal Pawar, Bob van de Water, Mark TD Cronin, and Gerard JP van Westen.
Computational Approaches for Drug-Induced Liver Injury (DILI) Prediction: State of the Art and Challenges.
In Reference Module in Biomedical Sciences. Elsevier, 2021. http://dx.doi.org/10.1016/B978-0-12-801238-3.11535-1
Liu, Xuhan, Adriaan P. IJzerman, and Gerard JP van Westen.
Computational approaches for de novo drug design: past, present, and future.
In Artificial Neural Networks, pp. 139-165. Humana, New York, NY, 2020. https://doi.org/10.1007/978-1-0716-0826-5_6
Bongers, Brandon J., Adriaan P. IJzerman, and Gerard JP Van Westen.
Proteochemometrics–recent developments in bioactivity and selectivity modeling.
Drug Discovery Today: Technologies 32 (2019): 89-98. https://doi.org/10.1016/j.ddtec.2020.08.003
Hebels, Dennie GAJ, Axel Rasche, Ralf Herwig, Gerard JP van Westen, Danyel GJ Jennen, and Jos CS Kleinjans.
A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.
In In Silico Methods for Predicting Drug Toxicity, pp. 339-359. Humana Press, New York, NY, 2016. https://doi.org/10.1007/978-1-4939-3609-0_15
Selected presentations
Unilever R&D (Vlaardingen, The Netherlands), March 2015 (Talk, invited)
LACDR Fall Symposium 2014 (Leiden, the Netherlands), October 2015 (Talk, invited)
Syngenta R&D Lunch Seminar (Bracknell, United Kingdom), November 2014 (Talk, invited)
Unilever R&D (Bedford, UK), May 2014 (Talk, invited)
10th International Conference on Chemical Structures 2014 (Noordwijkerhout, The Netherlands), June 2014 (Talk, contributed)
KNCV Medicinal Chemistry Spring Symposium 2014 (Utrecht, The Netherlands), March 2014 (Talk, invited)
FIGON Dutch Medicines Days 2013 (Ede, The Netherlands), October 2013 (Talk, invited)
Dutch Computers in Science Symposium (Amsterdam (KNAW)), The Netherlands, July 2013 (Talk, invited)
Heptares invited Lecture (Welwyn Garden City, UK), February 2013 (Talk, invited)
Edingburgh Meeting on Allostery (Edingburg, UK), December 2012 (Talk, invited)
Cambridge Cheminformatics Network Meeting (Cambridge, UK), August 2012 (Talk, invited)
Molsoft ICM User Group Meeting 2012 (San Diego, USA), March 2012 (Talk, invited)
FIGON Dutch Medicines Days 2011 (Lunteren, The Netherlands), October 2011 (Talk, invited)
ULLA Summer School (Parma, Italy), July 2011 (Talk, contributed)
TI-Pharma GPCR Forum Workshop (Driebergen, The Netherlands), June 2011 (Talk, invited)
9th International Conference on Chemical Structures (Noordwijkerhout, The Netherlands), June 2011 (Talk, contributed)
FIGON Dutch Medicines Days 2010 (Lunteren, The Netherlands), October 2010 (Talk, invited)
EuroQSAR 2010 (Rhodes, Greece), September 2010 (Talk, contributed)
5th German Conference on Cheminformatics (Goslar, Germany), November 2009 (Talk, contributed)
FIGON Dutch Medicines Days 2009 (Lunteren, The Netherlands), October 2009 (Poster, contributed)
FIGON Dutch Medicines Days 2008 (Lunteren, The Netherlands), October 2008 (Poster, contributed)
EuroQSAR 2008 (Uppsala, Sweden), September 2008 (Poster, contributed)
8th International Conference on Chemical Structures (Noordwijkerhout, The Netherlands), June 2008 (Poster, contributed)
Virtual Discovery Europe (Amsterdam, The Netherlands), July 2008 (Talk, contributed)
