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Gerard J. P. van Westen
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2020 – today
- 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) - [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 - 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)
2010 – 2019
- 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)
2000 – 2009
- 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)
Coauthor Index
aka: Herman W. T. van Vlijmen
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last updated on 2024-08-05 20:23 CEST by the dblp team
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