Gerard van Westen
Hoogleraar Artificial Intelligence & Medicinal Chemistry
- Naam
- Prof.dr. G.J.P. van Westen
- Telefoon
- +31 71 527 3511
- gerard@lacdr.leidenuniv.nl
- ORCID iD
- 0000-0003-0717-1817
Gerard van Westen is lid van het interdisciplinaire onderzoeksprogramma Society, Artificial Intelligence and Life Sciences (SAILS). Meer informatie is beschikbaar op de Engelstalige profielpagina.
Promovendi
Nieuws
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Oncode Accelerator van start: patiënt centraal bij innovatieve ontwikkeling kankermedicijnen -
Gerard van Westen wint KNCV Gouden Medaille -
Gerard van Westen bij EenVandaag: ‘AI helpt medicijnen sneller op de markt te krijgen’ -
Artificial intelligence als copiloot om medicijnen te vinden -
3 October University: ‘Kunstmatige intelligentie is net als seks onder jongeren’ -
Medicijnen maken met Kunstmatige Intelligentie als collega -
Hoe Oncode-PACT met 325 miljoen Groeifonds-geld nieuwe kankergeneesmiddelen dichterbij brengt -
Is een pil tegen kanker een kwestie van tijd? -
Gezondheid en zorg: AI-onderzoek in Leiden, Delft en Rotterdam -
Medical Delta AI for Computational Life Sciences -
Veiligheid van chemische stoffen en geneesmiddelen beoordelen zonder proefdieren -
Kersverse hoogleraar Gerard van Westen wil grenzen doorbreken
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Unieke medicijnstructuren vinden met kunstmatige intelligentie en scheikunde -
Efficiëntere geneesmiddelenontwikkeling met hulp van computermodellen -
NWO-subsidie voor slim computerprogramma dat speurt naar nieuwe medicijnen -
Drie Leidse samenwerkingsprojecten met het bedrijfsleven gehonoreerd -
Faculteit W&N versterkt de samenwerking met China -
Enorme databases doorlichten op zoek naar een medicijn tegen kanker -
14 Veni's voor Leidse wetenschappers
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Een beter begrip van het menselijk geheugen -
Ontdekker van het jaar, beste Proefschrift en Onderwijsprijs 2013
Oud-promovendi
Hoogleraar Artificial Intelligence & Medicinal Chemistry
- Wiskunde en Natuurwetenschappen
- Leiden Academic Centre for Drug Research
- LACDR/Medicinal Chemistry
- Mullowney M.W., Duncan K.R., Elsayed S.S., Garg N., Hooft J.J.J. van der, Martin N.I., Meijer D., Terlouw B.R., Biermann F., Blin K., Durairaj J., Gorostiola González M., Helfrich E.J.N., Huber F., Leopold-Messer S., Rajan K., Rond T. de, Santen J.A. van, Sorokina M., Balunas M.J., Beniddir M.A., Bergeijk D.A. van, Carroll L.M., Clark C.M., Clevert D.A., Dejong C.A., Du C., Ferrinho S., Grisoni F., Hofstetter A., Jespers W., Kalinina O.V., Kautsar S.A., Kim H., Leao T.F., Masschelein J., Rees E.R., Reher R., Reker D., Schwaller P., Segler M., Skinnider M.A., Walker A.S., Willighagen E.L., Zdrazil B., Ziemert N., Goss R.J.M., Guyomard P., Volkamer A., Gerwick W.H., Kim H.U., Müller R., Wezel G.P. van, Westen G.J.P. van, Hirsch A.K.H., Linington R.G., Robinson S.L. & Medema M.H. (2023), Artificial intelligence for natural product drug discovery, Nature Reviews Drug Discovery 22: 895–916.
- Béquignon O.J.M., Gómez-Tamayo J.C., Lenselink E.B., Wink S., Hiemstra S.W., Lam C.C., Gadaleta D., Roncaglioni A., Norinder U., Water B. van de, Pastor M. & Westen G.J.P. van (2023), Collaborative SAR modeling and prospective in vitro validation of oxidative stress activation in human HepG2 cells, Journal of Chemical Information and Modeling 63(17): 5433-5445.
- Houvast R.D., Badr N., March T., Muynck L.D.A.N. de, Sier V.Q., Schomann T., Bhairosingh S., Baart V.M., Peeters J.A.H.M., Westen G.J.P. van, Plückthun A., Burggraaf J., Kuppen P.J.K., Vahrmeijer A.L. & Sier C.F.M. (2023), 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 : .
- Gorostiola González M., Broek R.L. van den, Braun T.G.M., Chatzopoulou M., Jespers W., IJzerman A.P., Heitman L.H. & Westen G.J.P. van (2023), 3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors, Journal of cheminformatics 15(1): 74.
- Beerkens B.L.H., Snijders I.M., Snoeck J., Liu R., Tool A.T.J., Le Dévédec S.E., Jespers W., Kuijpers T.W., Westen G.J.P. van, Heitman L.H., IJzerman A.P. & Es D. van der (2023), Development of an affinity-based probe to profile endogenous human adenosine A3 receptor expression, Journal of Medicinal Chemistry 66(16): 11399-11413.
- Luukkonen S.I.M., Meijer E., Tricarico G.A., Hofmans J., Stouten P.F.W., Westen G.J.P. van & Lenselink E.B. (2023), Large-scale modeling of sparse protein kinase activity data, Journal of Chemical Information and Modeling 63(12): 3688-3696.
- Westen G.J.P. van (26 mei 2023). De computer als copiloot in de zoektocht naar nieuwe medicijnen. Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University. Leiden. [oratie].
- Luukkonen S.I.M., Maagdenberg H.W. van den, Emmerich M.T.M. & Westen G.J.P. van (2023), Artificial intelligence in multi-objective drug design, Current Opinion in Structural Biology 79: 102537.
- Bournez C., RioolM., Boer L. de, Cordfunke R.A., Best L. de, Leeuwen R. van, Drijfhout J.W., Zaat S.A.J. & Westen G.J.P. van (2023), CalcAMP: a new machine learning model for the accurate prediction of antimicrobial activity of peptides, Antibiotics 12(4): 725.
- Hollander L.S. den, Béquignon O.J.M., Wang X., Wezel K. van, Broekhuis J.D., Gorostiola Gonzalez M., Visser K.E. de, IJzerman A.P., Westen G.J.P. van & Heitman L.H. (2023), Corrigendum to "Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism" [Biochem. Pharmacol. 208 (2023) 115399], Biochemical Pharmacology 209: 115540 (115450).
- Sicho M., Luukkonena S., Maagdenberg H.W. van den, Schoenmaker L., Bequignon O.J.M. & Westen G.J.P. van (2023), DrugEx: deep learning models and tools for exploration of drug-like chemical space. [working paper].
- Bongers B.J., Sijben H.J., Hartog P.B.R., Tarnovskiy A., IJzerman A.P., Heitman L.H. & Westen G.J.P. van (2023), Proteochemometric modeling identifies chemically diverse norepinephrine transporter inhibitors, Journal of Chemical Information and Modeling 63(6): 1745-1755.
- Liu X., Ye K., Vlijmen H. van, IJzerman A.P. & Westen G.J.P. van (2023), DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning, Journal of Cheminformatics 15(1): 24.
- Schoenmaker L., Béquignon O.J.M., Jespers W. & Westen G.J.P. van (2023), UnCorrupt SMILES: a novel approach to de novo design, Journal of Cheminformatics 15(1): 22.
- Béquignon O.J.M., Bongers B.J., Jespers W., IJzerman A.P., Water B. van de & Westen G.J.P. van (2023), Papyrus: a large-scale curated dataset aimed at bioactivity predictions, Journal of cheminformatics 15(1): 3.
- Hollander L.S. den, Béquignon O.J.M., Wang X., Wezel K. van, Broekhuis J., Gorostiola González M., Visser K.E. de, IJzerman A.P., Westen G.J.P. van & Heitman L.H. (2022), Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism, Biochemical Pharmacology 208: 115399.
- Bongers B.J., Gorostiola González M., Wang X., Vlijmen H. van, Jespers W., Gutiérrez-de-Terán H., Ye K., IJzerman A.P., Heitman L.H. & Westen G.J.P. van (2022), Pan-cancer functional analysis of somatic mutations in G protein-coupled receptors, Scientific Reports 12(1): 21534.
- Wang X., Westen G.J.P. van, IJzerman A.P. & Heitman L.H. (2022), G protein-coupled receptors and their mutations in cancer: a focus on adenosine receptors. In: Gilchrist A. (red.) GPCRs as therapeutic targets.: John Wiley & Sons. 631-676.
- Liu Q., Stel W. van der, Noord V.E. van der, Leegwater H., Coban B., Elbertse K., Pruijs J.T.M., Béquignon O.J.M., Westen G.J.P. van, Dévédec S.E. le & Danen E.H.J. (2022), Hypoxia triggers TAZ phosphorylation in basal a triple negative breast cancer cells, International Journal of Molecular Sciences 23(17): 10119.
- Zwol W. van, Rimbert A., Wolters J.C., Smit M., Bloks V.W., Kloosterhuis N.J., Huijkman N.C.A., Koster M.H., Tharehalli U., Neck S.M. de, Bournez C., Fuh M.M., Kuipers J., Rajan S., Bruin A. de, Ginsberg H.N., Westen G.J.P. van, Hussain M.M., Scheja L., Heeren J., Zimmerman P., Sluis B. van de & Kuivenhoven J.A. (2023), Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion, Hepatology 78(5): 1418-1432.
- Hassing G.J., Esdonk M.J. van, Westen G.J.P. van, Cohen A.F., Burggraaf J. & Gal P. (2022), Dose escalations in phase I studies: feasibility of interpreting blinded pharmacodynamic data, British Journal of Clinical Pharmacology 88(12): 5412-5419.
- Feng C.L., Wang X., Jespers W., Liu R., Zamarbide Losada S.D., Gorostiola Gonzalez M., Westen G.J.P. van, Danen E.H.J. & Heitman L.H. (2022), Cancer-associated mutations of the adenosine A2A receptor have diverse influences on ligand binding and receptor functions, Molecules 27(15): 4676.
- Gorostiola Gonzalez M., Janssen A.P.A., IJzerman A.P., Heitman L.H. & Westen G.J.P. van (2022), Oncological drug discovery: AI meets structure-based computational research, Drug Discovery Today 27(6): 1661-1670.
- Wang X., Jespers W., Wolff K.A.N., Buytelaar J., IJzerman A.P., Westen G.J.P. van & Heitman L.H. (2022), Cancer-related somatic mutations in transmembrane helices alter adenosine A1 receptor pharmacology, Molecules 27(12): 3742.
- Qin T., Prins S., Groeneveld J.G., Westen G.J.P. van, Vries E.H. de, Wong C.Y., Bischoff L.J.M. & Lange E.C.M. de (2020), 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(9): 3158.
- Wall H.E.C. van der, Hassing G.J., Doll R.J., Westen G.J.P. van, Cohen A.F., Selder J.L., Kemme M., Burggraaf J. & Gal P. (2022), Cardiac age detected by machine learning applied to the surface ECG of healthy subjects: creation of a benchmark, Journal of Electrocardiology 72: 49-55.
- Wang X., Jespers W., Waal J.J. de, Wolff K.A.N., Uden L. van, IJzerman A.P., Westen G.J.P. van & Heitman L.H. (2022), Cancer-related somatic mutations alter adenosine A1 receptor pharmacology: a focus on mutations in the loops and C- terminus, The FASEB Journal 36(6): e22358.
- Tuerkova A., Bongers B.J., Norinder U., Ungvári O., Székely V., Tarnovskiy A., Szakács G., Özvegy-Laczka C., Westen G.J.P. van & Zdrazil B. (2022), Identifying novel inhibitors for hepatic organic anion transporting polypeptides by machine learning-based virtual screening, Journal of Chemical Information and Modeling 62(24): 6323-6335.
- Wall H.E.C. van der Doll R.J., Westen G.J.P. van, Niemeyer-van der Kolk T., Feiss G., Pinckaers H., Doorn M.B.A. van, Nijsten T., Sanders M.G.H., Cohen A.F., Burggraaf J., Rissmann R. & Pardo L.M. (2022), Discriminative machine learning analysis for skin microbiome: observing biomarkers in patients with seborrheic dermatitis, Journal of Artificial Intelligence for Medical Sciences 3(1-2): 1-7.
- Martens M., Stierum R., Schymanski E.L., Evelo C.T., Aalizadeh R., Aladjov H., Arturi K., Audouze K., Babica P., Berka K., Bessems J., Blaha L., Bolton E.E., Cases M., Damalas D.Ε., Dave K., Dilger M., Exner T., Geerke D.P., Grafström R., Gray A., Hancock J.M., Hollert H., Jeliazkova N., Jennen D., Jourdan F., Kahlem P., Klanova J., Kleinjans J., Kondic T., Kone B., Lynch I., Maran U., Martinez Cuesta S., Ménager H., Neumann S., Nymark P., Oberacher H., Ramirez N., Remy S., Rocca-Serra P., Salek R.M., Sallach B., Sansone S.A., Sanz F., Sarimveis H., Sarntivijai S., Schulze T., Slobodnik J., Spjuth O., Tedds J., Thomaidis N., Weber R.J.M., Westen G.J.P. van, Wheelock C.E., Williams A.J., Witters H., Zdrazil B., Županič A. & Willighagen E.L. (2021), ELIXIR and Toxicology: a community in development, F1000Research 10: 1129.
- Liu X., IJzerman A.P. & Westen G.J.P. van (2021), Computational Approaches for De Novo Drug Design: Past, Present, and Future. In: Cartwright H. (red.), Artificial Neural Networks. Methods in Molecular Biology nr. 2190. New York, NY, U.S.A.: Humana Press. 139-165.
- Jespers W., Heitman L.H., IJzerman A.P., Sotelo E., Westen G.J.P. van, Aqvist J. & Gutiérrez-de-Terán H. (2021), Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations, PLoS Computational Biology 17(11): e1009152.
- Liu X., Ye K., Vlijmen H.W.T. van, Emmerich M.T.M., IJzerman A.P. & Westen G.J.P. van (2021), DrugEx v2: de novo design of drug molecules by pareto-based multi-objective reinforcement learning in polypharmacology, Journal of Cheminformatics 13(1): 85.
- Martens M., Stierum R., Schymanski E.L., Evelo C.T., Aalizadeh R., Aladjov H., Arturi K., Audouze K., Babica P., Berka K., Bessems J., Blaha L., Bolton E.E., Cases M., Damalas D.Ε., Dave K., Dilger M., Exner T., Geerke Daan P., Grafström R., Gray A., Hancock J.M., Hollert H., Jeliazkova N., Jennen D., Jourdan F., Kahlem P., Klanova J., Kleinjans J., Kondic T., Kone B., Lynch I., Maran U., Martinez Cuesta S., Ménager H., Neumann S., Nymark P., Oberacher H., Ramirez N., Remy S., Rocca-Serra P., Salek R.M., Sallach B., Sansone S.A., Sanz F., Sarimveis H., Sarntivijai S., Schulze T., Slobodnik J., Spjuth O., Tedds J., Thomaidis N., Weber R.J.M., Westen G.J.P. van, Wheelock C.E., Williams A.J., Witters H., Zdrazil B., Županič A. & Willighagen E.L. (2021), ELIXIR and toxicology: a community in development, F1000Research 10: 1129.
- Sicho M., Liu X., Svozil D. & Westen G.J.P. van (2021), GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics, Journal of Cheminformatics 13(1): 73.
- Gao Y., Haren M.J., Buijs N., Innocent I., Zhang Y., Sartini D., Campagna R., Emanuelli M., Parsons R.B., Jespers W., Gutiérrez-de-Terán H., Westen G.J.P. van & Martin N.I. (2021), Potent inhibition of nicotinamide N-Methyltransferase by alkene-linked bisubstrate mimics bearing electron deficient aromatics, Journal of Medicinal Chemistry 64(17): 12938-12963.
- Wang X., Jespers W., Prieto-Díaz R., Majellaro M., IJzerman A.P., Westen G.J.P. van, Sotelo E. & Heitman L.H. (2021), Identification of V6.51L as a selectivity hotspot in stereoselective A2B adenosine receptor antagonist recognition, Scientific Reports 11.
- Tehrani K.H.M.E., Wade N., Mashayekhi V., Brüchle N.C., Jespers W., Voskuil K., Pesce D., Haren. M.J. van, Westen G.J.P. van & Martin N.I. (2021), Novel cephalosporin conjugates display potent and selective inhibition of imipenemase-type metallo-β-lactamases, Journal of Medicinal Chemistry 64(13): 9141-9151.
- Tehrani K.H.M.E., Wade N., Mashayekhi V., Brüchle N., Jespers W., Voskuil K., Pesce D., Haren M.J. van, Westen G.J.P. van & Martin N.I. (2021), Novel Cephalosporin conjugates display potent and selective inhibition of Imipenemase-type Metallo-β-Lactamases, Journal of Medicinal Chemistry 64(13): 9141–9151.
- Kovacikova K., Gorostiola González M., Jones R., Requera J., Gigante A., Pérez-Pérez M.J., Pürstinger G., Moesslacher J., Langer T., Jeong L.S., Delang L., Neyts J., Snijder E.J., Westen G.J.P. van & Hemert M.J. van (2021), Structural insights into the mechanisms of action of functionally distinct classes of chikungunya virus nonstructural protein 1 inhibitors, Antimicrobial Agents and Chemotherapy 65(7).
- Wall H.E.C. van der, Doll R.J., Westen G.J.P. van, Koopmans I., Zuiker R.G., Burggraaf J. & Cohen A.F. (2021), Using machine learning techniques to characterize sleep-deprived driving behavior, Traffic Injury Prevention 22(5): 366-371.
- Mohr F., Hurrle T., Burggraaff L., Langer L., Bemelmans M.P., Knab M., Nieger M., Westen G.J.P. van, Heitman L.H. & Bräse S. (2021), Synthesis and SAR evaluation of coumarin derivatives as potent cannabinoid receptor agonists, European Journal of Medicinal Chemistry 220.
- Amelia T., Veldhoven J.P.D. van, Falsini M., Liu R., Heitman L.H., Westen G.J.P. van, Segala E., Verdon G., Cheng R.K.Y., Cooke R.M., Es D. van der & IJzerman A.P. (2021), Crystal structure and subsequent ligand design of a nonriboside partial agonist bound to the adenosine A2A receptor, Journal of Medicinal Chemistry 64(7): 3827-3842.
- Leeuwen T. van, Araman C., Pournara L.P., Kampstra A.S.B., Bakkum T., Marqvorsen M.H.S., Nascimento C.R., Groenewold G.J.M., Wulp W. van der, Camps M.G.M., Janssen G.M.C., Veelen P.A. van, Westen G.J.P. van Janssen A.P.A., Florea B.I., Overkleeft H.S., Ossendorp F.A., Toes R.E.M. & Kasteren S.I. van (2021), Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens, RSC Chemical Biology 2(3): 855-862.
- Béquignon O.J.M., Pawara G., Water B. van de, Cronin M.T.D. & Westen G.J.P. van (2021), Computational approaches for drug-induced liver injury (DILI) prediction: state of the art and challenges. In: Wolkenhauer O. (red.) Systems Medicine. nr. 2: Elsevier. 308-329.
- Wang X., Westen G.J.P. van, Heitman L.H. & IJzerman A.P. (2021), G protein-coupled receptors expressed and studied in yeast. The adenosine receptor as a prime example, Biochemical Pharmacology 187: 114370.
- Fienieg B., Hassing G.J., Wall H.E.C. van der, Westen G.J.P. van, Kemme M.J.B., Adiyaman A., Elvan A., Burggraaf J. & Gal P. (2020), The association between body temperature and electrocardiographic parameters in normothermic healthy volunteers, Pace Pacing and Clinical Electrophysiology 44(1): 44-53.
- Burggraaff L., Veen A. van, Lam C.C., Vlijmen H.W.T., IJzerman A.P. & Westen G.J.P. van (2020), Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs, Journal of Chemical Information and Modeling 60(10): 4664-4672.
- Superti-Furga G., Lackner D., Wiedmer T., Ingles-Prieto A., Barbosa B., Girardi E., Goldmann U., Gürtl B., Klavins K., Klimek C., Lindinger S., Liñeiro-Retes E., Müller A.C., Onstein S., Redinger G., Reil D., Sedlyarov V., Wolf G., Crawford M., Everley R., Hepworth D., Liu S., Noell S., Piotrowski M., Stanton R., Zhang H., Corallino S., Faedo A., Insidioso M., Maresca G., Redaelli L., Sassone F., Scarabottolo L., Stucchi M., Tarroni P., Tremolada S., Batoulis H., Becker A., Bender E., Chang Y.N., Ehrmann A., Müller-Fahrnow A., Pütter V., Zindel D., Hamilton B., Lenter M., Santacruz D., Viollet C., Whitehurst C., Johnsson K., Leippe P., Baumgarten B., Chang L., Ibig Y., Pfeifer M., Reinhardt J., Schönbett J., Selzer P., Seuwen K., Bettembourg C., Biton B., Czech J., de Foucauld H., Didier M., Licher T., Mikol V., Pommereau A., Puech F., Yaligara V., Edwards A., Bongers B.J., Heitman L.H., Ijzerman A.P., Sijben H.J., Westen G.J.P. van, Grixti J., Kell D.B., Mughal F., Swainston N., Wright-Muelas M., Bohstedt T., Burgess-Brown N., Carpenter L., Dürr K., Hansen J., Scacioc A., Banci G., Colas C., Digles D., Ecker G., Füzi B., Gamsjäger V., Grandits M., Martini R., Troger F., Altermatt P., Doucerain C., Dürrenberger F., Manolova V., Steck A.L., Sundström H., Wilhelm M. & Steppan C.M. (2020), The RESOLUTE consortium: unlocking SLC transporters for drug discovery, Nature Reviews Drug Discovery 19(7): 429-430.
- Wang X. Jespers W. Bongers B.J. Habben Jansen M.C.C. Stangenberger C.M. Dilweg M.A. Gutiérrez-de-Terán H. IJzerman A.P. Heitman L.H. Westen G.J.P. van (2020), Characterization of cancer-related somatic mutations in the adenosine A2B receptor, European Journal of Pharmacology 880: 173126.
- Zhou J., Mock E.D., Al Ayed K., Di X., Kantae V., Burggraaff L., Stevens A.F., Martella A., Mohr F., Jiang M., Wel T. van der, Wendel T.J., Ofman T.P., Tran Y., Koster N. de, Westen G.J.P. van, Hankemeier T. & Stelt M. van der (2020), Structure-Activity Relationship Studies of α-Ketoamides as Inhibitors of the Phospholipase A and Acyltransferase Enzyme Family, Journal of Medicinal Chemistry 63(17): 9340-9359.
- Wel T. van der Hilhorst R Dulk H. den Hooven T. van den Prins N.M. Wijnakker J.A.P.M. Florea B.I. Lenselink E.B. Westen G.J.P. van Ruijtenbeek R. Overkleeft H.S. Kaptein A. Barf T. Stelt M. van der (2020), Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis, Nature Communications 11(1): 3216.
- Burggraaff L. Lenselink E.B. Jespers W. Engelen J. van Bongers B.J. Gorostiola Gonzalez M. Liu R. Hoos H.H. Vlijmen H. van IJzerman A.P. Westen G.J.P. van (2020), Successive statistical and structure-based modeling to identify chemically novel kinase inhibitors, Journal of Chemical Information and Modeling 60(9): 4283-4295.
- Škuta C., Cortés-Ciriano I., Dehaen W., Kříž P., Westen P.J.G. van, Tetko V.I., Bender A. & Svozil D. (2020), QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping, Journal of Cheminformatics 12: 39.
- Burggraaff L., Vlijmen H.W.T. van., IJzerman A.P. & Westen G.J.P. van (2020), Quantitative prediction of selectivity between the A1 and A2A adenosine receptors, Journal of Cheminformatics 12: 33.
- Wall H.E.C. van der, Doll R.J., Westen G.J.P. van der, Koopmans I., Zuiker R.G., Burggraaf J. & Cohen A.F. (2020), The use of machine learning improves the assessment of drug-induced driving behaviour, Accident Analysis and Prevention 148: 105822.
- Koenders S.T.A., Wijaya L.S., Erkelens M.N., Bakker A.T., Noord V.E. van der, Rooden E.J. van, Burggraaff L., Putter P.C., Botter E., Wals K., Elst H. van den, Dulk H. den, Florea B.I., Water B. van de, Westen G.J.P. van, Mebius R.E., Overkleeft H.S., Le Dévédec S.E. & Stelt M. van der (2019), Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells, ACS Central Science 5(12): 1965-1974.
- Malas T.B., Leonhard W.N., Bange H., Granchi Z., Hettne K.M., Westen G.J.P. van, Price L.S., Hoen P.A.C. 't & Peters D.J.M. (2020), Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles, EBioMedicine 51: 102585.
- Hassing G.J., Wall H.E.C. van der, Westen G.J.P. van, Kemme M.J.B., Adiyaman A., Elvan A., Burggraaf J. & Gal P. (2019), Blood pressure-related electrocardiographic findings in healthy young individuals, Blood Pressure 29(22): 113-122.
- Ruano‑Ordás D., Burggraaff L., Liu R., Horst C. van der, Heitman L.H., Emmerich M.T.M., Mendez J.R., Yevseyeva I. & Westen G.J.P. van (2019), A multiple classifier system identifies novel cannabinoid CB2 receptor ligands, Journal of Cheminformatics 11: 66.
- Oranje P., Gouka R., Burggraaff L., Vermeer M., Chalet C., Duchateau G., Pijl P. van der, Geldof M., Roo N. de, Clauwaert F., Vanpaeschen T., Nicolai J., Bruyn T. de, Annaert P., IJzerman A.P. & Westen G.J.P. van (2019), Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2, Pharmacology Research and Perspectives 7(4): e00504.
- Janssen A.P.A., Hengst J.M.A. van, Béquignon O.J.M., Deng H., Westen G.J.P. van & Stelt M. van der (2019), Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors, Journal of Medicinal Chemistry 62(17): 7910-7922.
- He J., McLaughlin R.P., Noord V.E. van der, Foekens J.A., Martens J.W.M., Westen G.J.P. van, Zhang Y. & Water B. van de (2019), Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer, Breast Cancer Research and Treatment 178(2): 263-274.
- Hameed D.S., Sapmaz A., Burggraaff L., Amore A., Slingerland C.J., Westen G.J.P. van & Ovaa H. (2019), Development of Ubiquitin-Based Probe for Metalloprotease Deubiquitinases, Angewandte Chemie (International Edition) 58(41): 14477-14482.
- Menden M.P., Wang D., Mason M.J., Szalai B., Bulusu K.C., Guan Y., Yu T., Kang J., Jeon M., Wolfinger R., Nguyen T., Zaslavskiy M., Jang I.S., Ghazoui Z., Ahsen M.E., Vogel R., Neto E.C., Norman T., Tang E.K.Y., Garnett M.J., Di Veroli G.Y., Fawell S., Stolovitzky G., Guinney J., Dry J.R., Saez-Rodriguez J. & Westen G.J.P. van (2019), Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen, Nature Communications 10: 2674.
- Booij T.H., Leonhard W.N., Bange H., Yan K., Fokkelman M., Plugge A.J., Veraar K.A.M., Dauwerse J.G., Westen G.J.P. van, Water B. van de, Price L.S. & Peters D.J.M. (2020), In vitro 3D phenotypic drug screen identifies celastrol as an effective in vivo inhibitor of polycystic kidney disease, Journal of Molecular Cell Biology 12(8): 644-653.
- Liu X., Ye K., Vlijmen H.W.T. van, IJzerman A.P. & Westen G.J.P. van (2019), An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor, Journal of Cheminformatics 11: 35.
- Hassing G.J., Wall H.E.C. van der, Westen G.J.P. van, Kemme M.J.B., Adiyaman A., Elvan A., Burggraaff J. & Gal P. (2019), Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index, Netherlands Heart Journal 27(10): 506-512.
- Sydow D., Burggraaff L., Szengel A., Vlijmen H. van, IJzerman A.P., Westen G.J.P. van & Volkamer A. (2019), Advances and Challenges in Computational Target Prediction, Journal of Chemical Information and Modeling 59(5): 1728-1742.
- Burggraaff L., Oranje P., Gouka R., Pijl P. van der, Geldof M., Vlijmen H.W.T. van, IJzerman A.P. & Westen G.J.P. van (2019), Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling, Journal of Cheminformatics 11: 15.
- Wall H.E.C. van der, Gal P., Kemme M.J.B., Westen G.J.P. van & Burggraaf J. (2019), Number of ECG Replicates Influences the Estimated QT Prolonging Effect of a Drug, Journal of Cardiovascular Pharmacology 73(4): 257-264.
- Grimm S.H., Gagestein B., Keijzer J.F., Liu N., Wijdeven R.H., Lenselink E.B., Tuin A.W., Nieuwendijk A.M.C.H. van den, Westen G.J.P. van, Boeckel C.A.A. van, Overkleeft H.S., Neefjes J. & Stelt M. van der (2019), Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors, Bioorganic & Medicinal Chemistry 27(5): 692-699.
- Zhou J., Mock E.D., Martella A., Kantae V., Di X., Burggraaff L., Baggelaar M.P., Al-Ayed K., Bakker A., Florea B.I., Grimm S.H., Dulk H. den, Li C.T., Mulder L., Overkleeft H.S., Westen G.J.P. van, Hankemeier T. & Stelt M. van der (2019), Activity-based protein profiling identifies α-ketoamides as inhibitors for Phospholipase A2 Group XVI, ACS Chemical Biology 14(2): 164-169.
- Bongers B.J., IJzerman A.P. & Westen G.J.P. (2019), Proteochemometrics – recent developments in bioactivity and selectivity modeling, Drug Discovery Today: Technologies 32-33: 89-98.
- Miggiels P., Wouters B., Westen G.J.P van, Dubbelman A.-C. & Hankemeier T. (2019), Novel technologies for metabolomics: More for less, Trends in Analytical Chemistry 120: 115323.
- Janssen A.P.A., Grimm S.H., Wijdeven R.H.M., Lenselink E.B., Neefjes J.J.C., Boeckel C.A.A. van, Westen G.J.P. van & Stelt M. van der (2019), Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes, Journal of Chemical Information and Modeling 59(3): 1221-1229.
- Pastor M., Westen G.J.P., Gomez-Tamayo J.C., Lenselink B.E., Lam C.-C., Water B. van de, Norinder U., Manganelli S., Gadaleta D. & Roncaglioni A. (2018), Development and validation of computational models for predicting oxidative stress responses using comprehensive series of drug-like compounds, Toxicology Letters 295(Supplement 1): S62-S63.
- Yang M., Simm J., Lam C.C., Zakeri P., Westen G.J.P. van, Moreau Y. & Saez-Rodriguez J. (2018), Linking drug target and pathway activation for effective therapy using multi-task learning, Scientific Reports 8(1): 8322.
- Tresadern G., Trabanco A.A., Pérez-Benito L., Overington J.P., Vlijmen H. van & Westen G.J.P. van (2017), Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling, Journal of Chemical Information and Modeling 57(12): 2976-2985.
- Jespers W., Schiedel A.C., Heitman L.H., Cooke R.M., Kleene L., Westen G.J.P. van, Gloriam D.E., Müller C.E., Sotelo E. & Gutiérrez-de-Terán H. (2018), Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms, Trends in Pharmacological Sciences 39(1): 75-89.
- Vlot A.H.C., Witte W.E.A. de, Danhof M., Graaf P.H. van der, Westen G.J.P. van & Lange E.C.M. de (2017), Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling, AAPS Journal 20(1): 11.
- Donkers J.M., Zehnder B., Westen G.J.P. van, Kwakkenbos M.J., IJzerman A.P., Oude Elferink R.P.J., Beuers U., Urban S. & Graaf S.F.J. van de (2017), Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP, Scientific Reports 7: 15307.
- Lenselink E.B., Dijke N. ten, Bongers B.J., Papadatos G., Vlijmen H. van, Kowalczyk W.J., IJzerman A.P. & Westen G.J.P. van (2017), Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set, Journal of Cheminformatics 9(1): 45.
- Booij T.H., Bange H., Leonhard W.N., Yan K., Fokkelman M., Kunnen S.J., Dauwerse J.G., Qin Y., Water B. van de, Westen G.J.P. van, Peters D.J.M. & Price L.S. (2017), High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease, Slas Discovery 22(8): 974-984.
- Hebels D.G., Rasche A., Herwig R., Westen G.J. van, Jennen D.G. & Kleinjans J.C. (2016), A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure. In: Benfenati E. (red.), In Silico Methods for Predicting Drug Toxicity. Methods in Molecular Biology nr. 1425. New York, NY: Humana Press. 339-359.
- Lenselink E.B., Jespers W., Vlijmen H.W.T. van, IJzerman A.P. & Westen G.J.P. van (2016), Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening, Journal of Chemical Information and Modeling 56(10): 2053-2060.
- Paricharak S.A., Méndez-Lucio O., Chavan Ravindranath A., Bender A., IJzerman A.P. & Westen G.J. van (2018), Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening, Briefings in Bioinformatics 19(2): 277-285.
- Christmann-Franck S., Westen G.J.P. van, Papadatos G., Escudie F.B., Roberts A., Overington J.P. & Domine D. (2016), Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design?, Journal of Chemical Information and Modeling 56(9): 1654-1675.
- Cortés-Ciriano I., Westen G.J.P. van, Bouvier B., Nilges M., Overington J.P., Bender A. & Malliavin T.E. (2016), Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel, Bioinformatics 32(1): 85-95.
- Murrell D.S., Cortes-Ciriano I., Westen G.J.P. van, Stott I.P., Bender A., Malliavin T.E. & Glen R.C. (2015), Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules, Journal of Cheminformatics 7: 45.
- Li P., Rial D., Canas P.M., Yoo J.-H., Li W., Zhou X., Wang Y., Westen G.J.P. van, Payen M.-P., Augusto E., Gonçalves N., Tomé A.R., Li Z., Wu Z., Hou X., Zhou Y., IJzerman A.P., Boyden E.S., Cunha R.A., Qu J. & Chen J.-.F. (2015), Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory, Molecular Psychiatry 20: 1339–1349.
- Cortes-Ciriano I., Westen G.J.P. van, Murrell D.S., Lenselink E.B., Bender A. & Malliavin T.E. (2015), Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling, BMC Bioinformatics 16(3): A4.
- Cortes-Ciriano I., Murrell D.S., Westen G.J.P. van, Bender A. & Malliavin T.E. (2015), Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling, Journal of Cheminformatics 7: 1.
- Gaulton A., Kale N., Westen G.J.P. van, Bellis L.J., Bento A.P., Davies M., Hersey A., Papadatos G., Forster M., Wege P. & Overington J.P. (2015), A large-scale crop protection bioassay data set, Scientific Data 2: 150032.
- Mugumbate G., Abrahams K., Cox J.A.G., Papadatos G., Westen G.J.P. van, Lelievre J., Calus S.T., Loman N., Ballel L., Barros D., Overington J.P. & Besra G.S. (2015), Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation, PLoS ONE 10(3): e0121492.
- Ain Qurrat U., Mendez-Lucio Oscar, Ciriano Isidro Cortes, Malliavin Therese, Van Westen Gerard J.P. & Bender Andreas (2014), 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(11): 1023-1033.
- Bansal M., Yang J., Karan C ., Menden M.P., Costello J.C., Tang H., Xiao G., Li Y., Allen J., Zhong R., Chen B., Kim M., Wang T., Heiser L.M., Realubit R., Mattioli M., Alvarez M.J., Shen Y., Westen G.J.P. van., IJzerman A.P., Lenselink E.B., Vlijmen H.W.T. van, Wegner J.K., Gallahan D., Singer D., Saez-Rodriguezc J., Xie Y., Stolovitzky G. & Califano A. (2014), A community computational challenge to predict the activity of pairs of compounds, Nature Biotechnology 32: 1213–1222.
- Peeters Miriam C., Li Qilan, Elands Rachel, Van Westen Gerard J.P., Lenselink Eelke B., Mueller Christa E. & IJzerman Adriaan P. (2014), Domains for activation and inactivation in G protein-coupled receptors - A mutational analysis of constitutive activity of the adenosine A(2B) receptor, Biochemical Pharmacology 92(2): 348-357.
- Cortes-Ciriano I., Ul Ain Q., Subramanian V., Lenselink E.B., Mendez-Lucio O., IJzerman A.P., Wohlfahrt G., Prusis P., Malliavin T.E., Westen G.J.P. van & Bender A. (2014), Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects, MedChemComm 6(1): 24-50.
- Davies M., Nowotka M., Papadatos G., Atkinson F., Westen G.J.P. van., Dedman N., Ochoa R. & Overington J.P. (2014), MyChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data, Challenges 5(2): 334-337.
- Lebedev A.V., Westman E., Westen G.J.P., Van Kramberger M.G., Lundervold A., Aarsland D., Soininen H., Kłoszewska I., Mecocci P., Tsolaki M., Vellas B., Lovestone S. & Simmons A . (2014), Random Forest ensembles for detection and prediction of Alzheimer's Disease with a good between-cohort robustness, NeuroImage: Clinical 6: 115-125.
- Papadatos G., Westen G.J.P van, Croset S., Santos S., Trubian S. & Overington J.P. (2014), A document classifier for medicinal chemistry publications trained on the ChEMBL corpus, Journal of Cheminformatics 6: 40.
- Kufareva I., Katritch V., Stevens R.C., Abagyan R. & et al (2014), Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges, Structure 22(8): 1120–1139.
- Cortes-Ciriano I., Westen G.J.P. van, Lenselink E.B., Murrel D.S., Bender A. & Malliavin T.E. (2014), Proteochemometric modeling in a Bayesian framework, Journal of Cheminformatics 6: 35.
- Costello J.C., Heiser L.M., Georgii E., Gönen M., Menden M.P., Wang N.J., Bansal M., Ammad-ud-din M., Hintsanen P., Khan S.A., Mpindi J-P., Kallioniemi O., Honkela A., Aittokallio T., Wennerberg K., Westen G.J.P van, Lenselink E.B., IJzerman A.P., Vlijmen H.W.T. van, Collins J.J., Gallahan D., Singer D., Saez-Rodriguez J., Kaski S., Gray J.W. & Stolovitzky G. (2014), A community effort to assess and improve drug sensitivity prediction algorithms, Nature Biotechnology 32: 1202–1212.
- Westen G.J.P. van, Bender A. & Overington J.P. (2014), Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling, Journal of Chemical Biology 7(4): 119-123.
- Westen G.J.P. van, Gaulton A. & Overington J.P. (2014), Chemical, target, and bioactive properties of allosteric modulation, PLoS Computational Biology 10(4): e1003559.
- Westen G.J.P. van, Swier R.F., Wegner J.K., IJzerman A.P., Vlijmen H. van & Bender A. (2013), Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets, Journal of Cheminformatics 5: 41.
- De Bruyn Tom, Van Westen Gerard J.P., IJzerman Adriaan P., Stieger Bruno, De Witte Peter, Augustijns Patrick F. & Annaert Pieter P. (2013), Structure-Based Identification of OATP1B1/3 Inhibitors, Molecular Pharmacology 83(6): 1257-1267.
- Westen G.J.P. van & Overington J.P. (2013), A ligand's-eye view of protein similarity, Nature Methods 10(2): 116-117.
- Westen G.J.P. van, Hendriks A., Wegner J.K., IJzerman A.P., Vlijmen H.W.T. van & Bender A. (2013), Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram, PLoS Computational Biology 9(2): e1002899.
- Westen G.J.P. van (8 januari 2013), Déjà Vu - Réjà Vu : on knowledge-based approaches linking ligand and target information to bioactivity (Dissertatie. Leiden/Amsterdam Center for Drug Research (LACDR), Faculty of Science, Leiden University). Promotor(en) en copromotor(en): IJzerman A.P. & Vlijmen H.W.T. van, Bender A.
- Van Westen Gerard J.P., Van den Hoven Olaf O., Van der Pijl Rianne, Mulder-Krieger Thea, De Vries Henk, Wegner Jorg K., Ijzerman Adriaan P., Van Vlijmen Herman W.T. & Bender Andreas (2012), Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data, Journal of Medicinal Chemistry 55(16): 7010-7020.
- Lane J. Robert, Herenbrink Carmen Klein, Van Westen Gerard J.P., Spoorendonk Jelle A., Hoffmann Carsten & IJzerman Adriaan P. (2012), A Novel Nonribose Agonist, LUF5834, Engages Residues That Are Distinct from Those of Adenosine-Like Ligands to Activate the Adenosine A(2a) Receptor, Molecular Pharmacology 81(3): 475-487.
- Peeters M.C., Li Q., Westen G.J.P. van & IJzerman A.P. (2012), Three "hotspots" important for adenosine A(2B) receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop, Purinergic Signalling 8(1): 23-38.
- Van der Horst E., Peironcely J.E., Van Westen G.J.P., Van den Hoven O.O., Galloway W.R.J.D., Spring D.R., Wegner J.K., Van Vlijmen H.W.T., IJzerman A.P., Overington J.P. & Bender A. (2011), Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space, Current Topics in Medicinal Chemistry 11(15): 1964-1977.
- Peeters M.C., Van Westen G.J., Guo D., Wisse L.E., Muller C.E., Beukers M.W. & IJzerman A.P. (2011), GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor, The FASEB Journal 25(2): 632-643.
- Peeters M.C., Van Westen G.J.P., Li Q. & IJzerman A.P. (2011), Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation, Trends in Pharmacological Sciences 32(1): 35-42.
- Van Westen G.J.P., Wegner J.K., IJzerman A.P., Van Vlijmen H.W.T. & Bender A. (2011), Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets, MedChemComm 2(1): 16-30.
- Westen G.J.P. van, Wegner J.K., Geluykens P., Kwanten L., Vereycken I., Peeters A., IJzerman A.P., Vlijmen H. van & Bender A. (2011), Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development, PLoS ONE 6(11): e27518.
- Doddareddy M.R., Westen G.J.P. van, Horst Eelke van der, Peironcely Julio E., Corthals Frans, IJzerman A.P., Emmerich Michael T.M., Jenkins Jeremy L. & Bender Andreas (2010), Chemogenomics: Looking at biology through the lens of chemistry, Statistical Analysis and Data Mining 2(3): 149-160.
- Van Westen G.J.P., Wegner J.K., Bender A., IJzerman A.P. & Van Vlijmen H.W.T. (2010), Mining protein dynamics from sets of crystal structures using "consensus structures", Protein Science 19(4): 742-752.
- Doddareddy M.R., Westen G.J.P. van, Horst E. van der, Peironcely J., Corthals F., IJzerman A.P., Emmerich M.T.M., Jenkins J.L. & Bender A. (2009), Chemogenomics: Looking at biology through the lens of chemistry, Statistical Analysis and Data Mining 2(3): 149-160.
- Scientific Advisory Board Member
- Guest Editor
- Guest Researcher
- Organizing committee member
- Data mining and analytics consultancy