Gerard J. P. van Westen

According to our database, Gerard J. P. van Westen authored at least 42 papers between 2009 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool.

Helle W. van den Maagdenberg, Martin Sícho, David Alencar Araripe, Sohvi Luukkonen, Linde Schoenmaker, Michiel Jespers, Olivier J. M. Béquignon, Marina Gorostiola González, Remco L. van den Broek, Andrius Bernatavicius, J. G. Coen van Hasselt, Piet H. Van Der Graaf, Gerard J. P. van Westen

J. Cheminformatics, December, 2024

AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models.

Andrius Bernatavicius, Martin Sícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuss, Gerard J. P. van Westen

J. Chem. Inf. Model., 2024

2023

UnCorrupt SMILES: a novel approach to de novo design.

Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers, Gerard J. P. van Westen

J. Cheminformatics, December, 2023

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning.

Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen

J. Cheminformatics, December, 2023

3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors.

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

J. Cheminformatics, December, 2023

Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells.

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

J. Chem. Inf. Model., September, 2023

DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space.

Martin Sícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen

J. Chem. Inf. Model., June, 2023

Large-Scale Modeling of Sparse Protein Kinase Activity Data.

Sohvi Luukkonen, Erik Meijer, Giovanni Tricarico, Johan Hofmans, Pieter F. W. Stouten, Gerard J. P. van Westen, Eelke B. Lenselink

J. Chem. Inf. Model., June, 2023

Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors.

Brandon J. Bongers, Huub J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen

J. Chem. Inf. Model., March, 2023

Papyrus: a large-scale curated dataset aimed at bioactivity predictions.

Olivier J. M. Béquignon, Brandon J. Bongers, Willem Jespers, Adriaan P. IJzerman, B. van der Water, Gerard J. P. van Westen

J. Cheminformatics, 2023

2022

Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening.

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

J. Chem. Inf. Model., 2022

2021

Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations.

Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán

PLoS Comput. Biol., 2021

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics.

Martin Sícho, Xuhan Liu, Daniel Svozil, Gerard J. P. van Westen

J. Cheminformatics, 2021

DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology.

Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen

J. Cheminformatics, 2021

Computational Approaches for De Novo Drug Design: Past, Present, and Future.

Xuhan Liu, Adriaan P. IJzerman, Gerard J. P. van Westen

Proceedings of the Artificial Neural Networks - Third Edition., 2021

2020

Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs.

Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen

J. Chem. Inf. Model., 2020

Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors.

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

J. Chem. Inf. Model., 2020

QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping.

Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil

J. Cheminformatics, 2020

Quantitative prediction of selectivity between the A₁ and A_2A adenosine receptors.

Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen

J. Cheminformatics, 2020

2019

Advances and Challenges in Computational Target Prediction.

Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer

J. Chem. Inf. Model., 2019

Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes.

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

J. Chem. Inf. Model., 2019

A multiple classifier system identifies novel cannabinoid CB2 receptor ligands.

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

J. Cheminformatics, 2019

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor.

Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen

J. Cheminformatics, 2019

Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.

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

J. Cheminformatics, 2019

2018

Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening.

Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen

Briefings Bioinform., 2018

2017

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.

Gary Tresadern, Andrés A. Trabanco, Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, Gerard J. P. van Westen

J. Chem. Inf. Model., December, 2017

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.

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

J. Cheminformatics, 2017

2016

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening.

Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen

J. Chem. Inf. Model., 2016

Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design?

Serge Christmann-Franck, Gerard J. P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, Daniel Domine

J. Chem. Inf. Model., 2016

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin

Bioinform., 2016

2015

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.

Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen

J. Cheminformatics, 2015

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.

Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin

J. Cheminformatics, 2015

Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling.

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin

BMC Bioinform., 2015

2014

Chemical, Target, and Bioactive Properties of Allosteric Modulation.

Gerard J. P. van Westen, Anna Gaulton, John P. Overington

PLoS Comput. Biol., 2014

A document classifier for medicinal chemistry publications trained on the ChEMBL corpus.

George Papadatos, Gerard J. P. van Westen, Samuel Croset, Rita Santos, Simone Trubian, John P. Overington

J. Cheminformatics, 2014

Proteochemometric modeling in a Bayesian framework.

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin

J. Cheminformatics, 2014

2013

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data.

Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender

PLoS Comput. Biol., 2013

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets.

Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender

J. Cheminformatics, 2013

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.

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

J. Cheminformatics, 2013

2010

Molecular bioactivity extrapolation to novel targets by support vector machines.

Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender

J. Cheminformatics, 2010

Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models.

Olaf van den Hoven, Gerard J. P. van Westen, Andreas Bender

J. Cheminformatics, 2010

2009

Chemogenomics: Looking at biology through the lens of chemistry.

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

Stat. Anal. Data Min., 2009