Search Results - "GERARD, J. P"

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

“…The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches…”
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2023 A new French revolution: Organ preservation for rectal cancer by Gérard, J.-P.

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Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel by Cortés-Ciriano, Isidro, van Westen, Gerard J P, Bouvier, Guillaume, Nilges, Michael, Overington, John P, Bender, Andreas, Malliavin, Thérèse E

“…Recent large-scale omics initiatives have catalogued the somatic alterations of cancer cell line panels along with their pharmacological response to hundreds…”
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Expand Your Horizon: A programme that improves body image and reduces self-objectification by training women to focus on body functionality by Alleva, Jessica M., Martijn, Carolien, Van Breukelen, Gerard J.P., Jansen, Anita, Karos, Kai

“…•We conducted a randomised controlled trial of the Expand Your Horizon programme.•The programme teaches participants to focus on the functionality of their…”
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Advances and Challenges in Computational Target Prediction by Sydow, Dominique, Burggraaff, Lindsey, Szengel, Angelika, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P, Volkamer, Andrea

“…Target deconvolution is a vital initial step in preclinical drug development to determine research focus and strategy. In this respect, computational target…”
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An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor by Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.

“…Over the last 5 years deep learning has progressed tremendously in both image recognition and natural language processing. Now it is increasingly applied to…”
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Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities by Gorostiola González, Marina, Rakers, Pepijn R J, Jespers, Willem, IJzerman, Adriaan P, Heitman, Laura H, van Westen, Gerard J P

“…Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but…”
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DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology by Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., Emmerich, Michael T. M., IJzerman, Adriaan P., van Westen, Gerard J. P.

“…In polypharmacology drugs are required to bind to multiple specific targets, for example to enhance efficacy or to reduce resistance formation. Although deep…”
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Cluster Randomized Trials with a Pretest and Posttest: Equivalence of Three-, Two- and One-Level Analyses, and Sample Size Calculation by Van Breukelen, Gerard J. P.

“…In a cluster randomized trial clusters of persons, for instance, schools or health centers, are assigned to treatments, and all persons in the same cluster get…”
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Potent Inhibition of Nicotinamide N‑Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics by Gao, Yongzhi, van Haren, Matthijs J, Buijs, Ned, Innocenti, Paolo, Zhang, Yurui, Sartini, Davide, Campagna, Roberto, Emanuelli, Monica, Parsons, Richard B, Jespers, Willem, Gutiérrez-de-Terán, Hugo, van Westen, Gerard J. P, Martin, Nathaniel I

“…Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide (vitamin B3) to generate 1-methylnicotinamide (MNA). NNMT overexpression has been linked to a…”
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Computational Approaches for De Novo Drug Design: Past, Present, and Future by Liu, Xuhan, IJzerman, Adriaan P, van Westen, Gerard J P

“…Drug discovery is time- and resource-consuming. To this end, computational approaches that are applied in de novo drug design play an important role to improve…”
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AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models by Bernatavicius, Andrius, Šícho, Martin, Janssen, Antonius P. A., Hassen, Alan Kai, Preuss, Mike, van Westen, Gerard J. P.

“…Recent advancements in deep learning and generative models have significantly expanded the applications of virtual screening for drug-like compounds. Here, we…”
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DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning by Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.

“…Rational drug design often starts from specific scaffolds to which side chains/substituents are added or modified due to the large drug-like chemical space…”
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Development of Ubiquitin‐Based Probe for Metalloprotease Deubiquitinases by Hameed, Dharjath S., Sapmaz, Aysegul, Burggraaff, Lindsey, Amore, Alessia, Slingerland, Cornelis J., Westen, Gerard J. P., Ovaa, Huib

“…Deubiquitinases (DUBs) are a family of enzymes that regulate the ubiquitin signaling cascade by removing ubiquitin from specific proteins in response to…”
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Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP by Donkers, Joanne M., Zehnder, Benno, van Westen, Gerard J. P., Kwakkenbos, Mark J., IJzerman, Adriaan P., Oude Elferink, Ronald P. J., Beuers, Ulrich, Urban, Stephan, van de Graaf, Stan F. J.

“…The sodium taurocholate co-transporting polypeptide (NTCP, SLC10A1 ) is the main hepatic transporter of conjugated bile acids, and the entry receptor for…”
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Linking drug target and pathway activation for effective therapy using multi-task learning by Yang, Mi, Simm, Jaak, Lam, Chi Chung, Zakeri, Pooya, van Westen, Gerard J. P., Moreau, Yves, Saez-Rodriguez, Julio

“…Despite the abundance of large-scale molecular and drug-response data, the insights gained about the mechanisms underlying treatment efficacy in cancer has…”
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Identifying patient subgroups in MASLD and MASH-associated fibrosis: molecular profiles and implications for drug development by González Hernández, Manuel A., Verschuren, Lars, Caspers, Martien P.M., Morrison, Martine C., Venhorst, Jennifer, van den Berg, Jelle T., Coornaert, Beatrice, Hanemaaijer, Roeland, van Westen, Gerard J. P.

“…The incidence of MASLD and MASH-associated fibrosis is rapidly increasing worldwide. Drug therapy is hampered by large patient variability and partial…”
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Identification of V6.51L as a selectivity hotspot in stereoselective A2B adenosine receptor antagonist recognition by Wang, Xuesong, Jespers, Willem, Prieto-Díaz, Rubén, Majellaro, Maria, IJzerman, Adriaan P., van Westen, Gerard J. P., Sotelo, Eddy, Heitman, Laura H., Gutiérrez-de-Terán, Hugo

“…The four adenosine receptors (ARs) A 1 AR, A 2A AR, A 2B AR , and A 3 AR are G protein-coupled receptors (GPCRs) for which an exceptional amount of…”
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Specialised treatment based on cognitive behaviour therapy versus usual care for tinnitus: a randomised controlled trial by Cima, Rilana FF, Dr, Maes, Iris H, MSc, Joore, Manuela A, PhD, Scheyen, Dyon JWM, MSc, El Refaie, Amr, PhD, Baguley, David M, PhD, Anteunis, Lucien JC, PhD, van Breukelen, Gerard JP, PhD, Vlaeyen, Johan WS, PhD

“…Summary Background Up to 21% of adults will develop tinnitus, which is one of the most distressing and debilitating audiological problems. The absence of…”
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Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-β-Lactamases by Tehrani, Kamaleddin H. M. E, Wade, Nicola, Mashayekhi, Vida, Brüchle, Nora C, Jespers, Willem, Voskuil, Koen, Pesce, Diego, van Haren, Matthijs J, van Westen, Gerard J. P, Martin, Nathaniel I

“…In an attempt to exploit the hydrolytic mechanism by which β-lactamases degrade cephalosporins, we designed and synthesized a series of novel cephalosporin…”
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