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Journal Articles
- 2023
[j39]Olivier J. M. Béquignon
, Brandon J. Bongers, Willem Jespers, Adriaan P. IJzerman, B. van der Water, Gerard J. P. van Westen:
Papyrus: a large-scale curated dataset aimed at bioactivity predictions. J. Cheminformatics 15(1): 3 (2023)- [j38]Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers, Gerard J. P. van Westen:
UnCorrupt SMILES: a novel approach to de novo design. J. Cheminformatics 15(1): 22 (2023) - [j37]Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. J. Cheminformatics 15(1): 24 (2023) - [j36]Marina Gorostiola González, Remco L. van den Broek, Thomas G. M. Braun, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen:
3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors. J. Cheminformatics 15(1): 74 (2023) - [j35]Brandon J. Bongers, Huub J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen:
Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. J. Chem. Inf. Model. 63(6): 1745-1755 (2023) - [j34]Martin Sícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen:
DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. J. Chem. Inf. Model. 63(12): 3629-3636 (2023) - [j33]Sohvi Luukkonen, Erik Meijer, Giovanni Tricarico, Johan Hofmans, Pieter F. W. Stouten, Gerard J. P. van Westen, Eelke B. Lenselink:
Large-Scale Modeling of Sparse Protein Kinase Activity Data. J. Chem. Inf. Model. 63(12): 3688-3696 (2023) - [j32]Olivier J. M. Béquignon, Jose C. Gómez-Tamayo, Eelke B. Lenselink, Steven Wink, Steven Hiemstra, Chi Chung Lam, Domenico Gadaleta, Alessandra Roncaglioni, Ulf Norinder, Bob van de Water, Manuel Pastor, Gerard J. P. van Westen:
Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells. J. Chem. Inf. Model. 63(17): 5433-5445 (2023) - 2022
- [j31]Alzbeta Türková, Brandon J. Bongers, Ulf Norinder, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, Gergely Szakács, Csilla Özvegy-Laczka, Gerard J. P. van Westen, Barbara Zdrazil:
Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening. J. Chem. Inf. Model. 62(24): 6323-6335 (2022) - 2021
- [j30]Martin Sícho, Xuhan Liu, Daniel Svozil, Gerard J. P. van Westen:
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. J. Cheminformatics 13(1): 73 (2021) - [j29]Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen:
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. J. Cheminformatics 13(1): 85 (2021) - [j28]Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán:
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. PLoS Comput. Biol. 17(11) (2021) - 2020
- [j27]Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. J. Cheminformatics 12(1): 33 (2020) - [j26]Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. J. Cheminformatics 12(1): 39 (2020) - [j25]Lindsey Burggraaff, Eelke B. Lenselink, Willem Jespers, Jesper E. van Engelen, Brandon J. Bongers, Marina Gorostiola González, Rongfang Liu, Holger H. Hoos, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. J. Chem. Inf. Model. 60(9): 4283-4295 (2020) - [j24]Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. J. Chem. Inf. Model. 60(10): 4664-4672 (2020) - 2019
- [j23]Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. J. Cheminformatics 11(1): 15:1-15:10 (2019) - [j22]Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, 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. Cheminformatics 11(1): 35:1-35:16 (2019) - [j21]David Ruano-Ordás, Lindsey Burggraaff, Rongfang Liu, Cas van der Horst, Laura H. Heitman, Michael T. M. Emmerich, José Ramón Méndez, Iryna Yevseyeva, Gerard J. P. van Westen:
A multiple classifier system identifies novel cannabinoid CB2 receptor ligands. J. Cheminformatics 11(1): 66:1-66:14 (2019) - [j20]Antonius P. A. Janssen, Sebastian H. Grimm, Ruud H. M. Wijdeven, Eelke B. Lenselink, Jacques Neefjes, Constant A. A. van Boeckel, Gerard J. P. van Westen, Mario van der Stelt:
Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes. J. Chem. Inf. Model. 59(3): 1221-1229 (2019) - [j19]Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer:
Advances and Challenges in Computational Target Prediction. J. Chem. Inf. Model. 59(5): 1728-1742 (2019) - 2018
- [j18]Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen:
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings Bioinform. 19(2): 277-285 (2018) - 2017
- [j17]Eelke B. Lenselink, Niels ten Dijke, Brandon J. Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, Gerard J. P. van Westen:
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. J. Cheminformatics 9(1): 45 (2017) - [j16]Gary Tresadern, Andrés A. Trabanco, Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, Gerard J. P. van Westen:
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. J. Chem. Inf. Model. 57(12): 2976-2985 (2017) - 2016
- [j15]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin:
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinform. 32(1): 85-95 (2016) - [j14]Serge Christmann-Franck, Gerard J. P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, Daniel Domine:
Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? J. Chem. Inf. Model. 56(9): 1654-1675 (2016) - [j13]Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. J. Chem. Inf. Model. 56(10): 2053-2060 (2016) - 2015
- [j12]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin:
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. BMC Bioinform. 16(S-3): A4 (2015) - [j11]Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin:
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. J. Cheminformatics 7: 1 (2015) - [j10]Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen:
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. J. Cheminformatics 7: 45:1-45:10 (2015) - 2014
- [j9]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin:
Proteochemometric modeling in a Bayesian framework. J. Cheminformatics 6(1): 35 (2014) - [j8]George Papadatos, Gerard J. P. van Westen, Samuel Croset, Rita Santos, Simone Trubian, John P. Overington:
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus. J. Cheminformatics 6(1): 40 (2014) - [j7]Gerard J. P. van Westen, Anna Gaulton, John P. Overington:
Chemical, Target, and Bioactive Properties of Allosteric Modulation. PLoS Comput. Biol. 10(4) (2014) - 2013
- [j6]Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. J. Cheminformatics 5: 41 (2013) - [j5]Gerard J. P. van Westen, Remco F. Swier, Isidro Cortes-Ciriano, Jörg K. Wegner, John P. Overington, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics 5: 42 (2013) - [j4]Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. PLoS Comput. Biol. 9(2) (2013) - 2010
- [j3]Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Molecular bioactivity extrapolation to novel targets by support vector machines. J. Cheminformatics 2(S-1): 3 (2010) - [j2]Olaf van den Hoven, Gerard J. P. van Westen, Andreas Bender:
Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models. J. Cheminformatics 2(S-1): 16 (2010) - 2009
- [j1]Munikumar R. Doddareddy, Gerard J. P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. IJzerman, Michael Emmerich, Jeremy L. Jenkins, Andreas Bender:
Chemogenomics: Looking at biology through the lens of chemistry. Stat. Anal. Data Min. 2(3): 149-160 (2009)
Parts in Books or Collections
- 2021
- [p1]Xuhan Liu, Adriaan P. IJzerman, Gerard J. P. van Westen:
Computational Approaches for De Novo Drug Design: Past, Present, and Future. Artificial Neural Networks, 3rd Edition 2021: 139-165
Coauthor Index
aka: Herman W. T. van Vlijmen
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