List of works - Gerard J. P. van Westen

Development of an Affinity-Based Probe to Profile Endogenous Human Adenosine A3 Receptor Expression

scientific article published on 2 August 2023

A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure

scientific article published on January 2016

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

scientific article (publication date: December 2014)

A large-scale crop protection bioassay data set

scientific article

A ligand's-eye view of protein similarity ⬇️

scientific article published on February 1, 2013

A multiple classifier system identifies novel cannabinoid CB2 receptor ligands

scientific article published on 7 November 2019

A novel nonribose agonist, LUF5834, engages residues that are distinct from those of adenosine-like ligands to activate the adenosine A(2a) receptor.

scientific article

Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI

scientific article published on 18 January 2019

Advances and Challenges in Computational Target Prediction

scientific article published on 28 February 2019

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

scientific article published on 24 May 2019

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

scientific article published on 15 September 2020

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

article

Artificial intelligence for natural product drug discovery ⬇️

scientific article from 2023

Artificial intelligence in multi-objective drug design

scientific article published in April 2023

Author Correction: Linking drug target and pathway activation for effective therapy using multi-task learning

scholarly article published in Scientific Reports

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

scientific article published on 23 September 2013

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

scientific article published on 24 September 2013

Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set

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

scientific article published on 14 August 2017

Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens

scientific article

Blood pressure-related electrocardiographic findings in healthy young individuals

scientific article published on 12 November 2019

Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index

scientific article published on 01 October 2019

CalcAMP: A New Machine Learning Model for the Accurate Prediction of Antimicrobial Activity of Peptides

scientific article published on 7 April 2023

Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions

scientific article published on 22 July 2022

Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology

scientific article published on 10 June 2022

Cardiac age detected by machine learning applied to the surface ECG of healthy subjects: Creation of a benchmark

scientific article published in 2022

Characterization of cancer-related somatic mutations in the adenosine A2B receptor

scientific article published on 26 April 2020

Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis

scientific article published on 25 June 2020

Chemical, target, and bioactive properties of allosteric modulation

scientific article (publication date: April 2014)

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

scientific article (publication date: 2015)

Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space

scientific article published on January 2011

Chemogenomics: Looking at biology through the lens of chemistry

Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors

scientific article published on 14 January 2019

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

scientific article published on 01 January 2021

Crystal Structure and Subsequent Ligand Design of a Nonriboside Partial Agonist Bound to the Adenosine A2A Receptor

scientific article published on 25 March 2021

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

scientific article published in March 2018

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

scientific article published on 24 November 2021

Development of Ubiquitin-Based Probe for Metalloprotease Deubiquitinases

scientific article published on 28 August 2019

Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells

scientific article published on 12 December 2019

Domains for activation and inactivation in G protein-coupled receptors--a mutational analysis of constitutive activity of the adenosine A2B receptor

scientific article

Drug Discovery Maps, a machine learning model, visualizes and predicts kinome-inhibitor interaction landscapes

scientific article published on 08 November 2018

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

scientific article

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

scientific article published on 5 June 2023

Déjà Vu - Réjà Vu ⬇️

thesis

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

G protein-coupled receptors expressed and studied in yeast. The adenosine receptor as a prime example

scientific article published on 15 December 2020

GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor

scholarly article published February 2011

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

scientific article published in 2021

High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease

Hypoxia Triggers TAZ Phosphorylation in Basal A Triple Negative Breast Cancer Cells

scientific article published on 4 September 2022

IN VITRO 3D PHENOTYPIC DRUG SCREEN IDENTIFIES CELASTROL AS AN EFFECTIVE IN VIVO INHIBITOR OF POLYCYSTIC KIDNEY DISEASE

scientific article published on 08 May 2019

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

scientific article published on 26 November 2017

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

scientific article published on 14 February 2019

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

scientific article published on 11 March 2022

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data

scientific article

Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation

scientific article (publication date: 2011)

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

scientific article

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening

scientific article published on 24 October 2016

Large-Scale Modeling of Sparse Protein Kinase Activity Data

scientific article published on 9 June 2023

Linking drug target and pathway activation for effective therapy using multi-task learning.

scientific article published on 29 May 2018

Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion

scientific article published on 12 October 2022

Mining protein dynamics from sets of crystal structures using "consensus structures".

scientific article published on April 2010

Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features

scientific article published in November 2014

Molecular bioactivity extrapolation to novel targets by support vector machines.

scientific article published on 4 May 2010

Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer

scientific article published on 06 August 2019

MyChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

scientific article

Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-β-Lactamases

scientific article published on 28 June 2021

Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2

scientific article published on 30 July 2019

Novel technologies for metabolomics: More for less

article by Paul Miggiels et al published November 2018 in Trends in Analytical Chemistry

Number of ECG Replicates and QT Correction Formula Influences the Estimated QT Prolonging Effect of a Drug

scientific article published on 01 April 2019

Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory

scientific article

Pan-cancer in silico analysis of somatic mutations in G-protein coupled receptors: The effect of evolutionary conservation and natural variance

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

scientific article published on 6 January 2023

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

article

Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics

scientific article

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

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

scientific article

Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles

scientific article published on 24 December 2019

Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors

scientific article published on 16 March 2023

Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

article

Proteochemometric modeling in a Bayesian framework

scientific article published on 28 June 2014

Proteochemometrics - recent developments in bioactivity and selectivity modeling

scientific article published on 01 December 2019

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

scientific article published on 29 May 2020

Quantitative prediction of selectivity between the A1 and A2A adenosine receptors

scientific article published on 13 May 2020

Random Forest ensembles for detection and prediction of Alzheimer's disease with a good between-cohort robustness

scientific article

Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP.

scientific article

Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data

scientific article

Structural Insights into the Mechanisms of Action of Functionally Distinct Classes of Chikungunya Virus Nonstructural Protein 1 Inhibitors

scientific article published on 17 June 2021

Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms

scientific article published in December 2017

Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors

scientific article published on 30 August 2019

Structure-Activity Relationship Studies of α-Ketoamides as Inhibitors of the Phospholipase A and Acyltransferase Enzyme Family

scientific article published on 13 August 2020

Structure-based identification of OATP1B1/3 inhibitors

scientific article

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

scientific article published on 28 April 2020

Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling.

scientific article published on 4 December 2017

The RESOLUTE consortium: unlocking SLC transporters for drug discovery

scientific article published on 07 April 2020

The association between body temperature and electrocardiographic parameters in normothermic healthy volunteers

scientific article published on 12 November 2020

Three "hotspots" important for adenosine A(2B) receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop

scientific article published on 5 August 2011

Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling

scientific article

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

scientific article published on 2 August 2016

Utility of Animal Models to Understand Human Alzheimer's Disease, Using the Mastermind Research Approach to Avoid Unnecessary Further Sacrifices of Animals

scientific article published on 30 April 2020

Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development

scientific article

List of works by Gerard J. P. van Westen

<b>Development of an Affinity-Based Probe to Profile Endogenous Human Adenosine A<sub>3</sub> Receptor Expression</b>

A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure

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

A large-scale crop protection bioassay data set

A ligand's-eye view of protein similarity ⬇️

A multiple classifier system identifies novel cannabinoid CB2 receptor ligands

A novel nonribose agonist, LUF5834, engages residues that are distinct from those of adenosine-like ligands to activate the adenosine A(2a) receptor.

Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI

Advances and Challenges in Computational Target Prediction

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

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

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

Artificial intelligence for natural product drug discovery ⬇️

Artificial intelligence in multi-objective drug design

Author Correction: Linking drug target and pathway activation for effective therapy using multi-task learning

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

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

Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set

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

Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens

Blood pressure-related electrocardiographic findings in healthy young individuals

Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index

CalcAMP: A New Machine Learning Model for the Accurate Prediction of Antimicrobial Activity of Peptides

Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions

Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology

Cardiac age detected by machine learning applied to the surface ECG of healthy subjects: Creation of a benchmark

Characterization of cancer-related somatic mutations in the adenosine A2B receptor

Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis

Chemical, target, and bioactive properties of allosteric modulation

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

Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space

Chemogenomics: Looking at biology through the lens of chemistry

Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors

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

Crystal Structure and Subsequent Ligand Design of a Nonriboside Partial Agonist Bound to the Adenosine A<sub>2A</sub> Receptor

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

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

Development of Ubiquitin-Based Probe for Metalloprotease Deubiquitinases

Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells

Domains for activation and inactivation in G protein-coupled receptors--a mutational analysis of constitutive activity of the adenosine A2B receptor

Drug Discovery Maps, a machine learning model, visualizes and predicts kinome-inhibitor interaction landscapes

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

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

Déjà Vu - Réjà Vu ⬇️

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

G protein-coupled receptors expressed and studied in yeast. The adenosine receptor as a prime example

GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor

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

High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease

Hypoxia Triggers TAZ Phosphorylation in Basal A Triple Negative Breast Cancer Cells

IN VITRO 3D PHENOTYPIC DRUG SCREEN IDENTIFIES CELASTROL AS AN EFFECTIVE IN VIVO INHIBITOR OF POLYCYSTIC KIDNEY DISEASE

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

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

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

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data

Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation

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

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening

Large-Scale Modeling of Sparse Protein Kinase Activity Data

Linking drug target and pathway activation for effective therapy using multi-task learning.

Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion

Mining protein dynamics from sets of crystal structures using "consensus structures".

Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features

Molecular bioactivity extrapolation to novel targets by support vector machines.

Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer

MyChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-β-Lactamases

Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2

Novel technologies for metabolomics: More for less

Number of ECG Replicates and QT Correction Formula Influences the Estimated QT Prolonging Effect of a Drug

Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory

Pan-cancer in silico analysis of somatic mutations in G-protein coupled receptors: The effect of evolutionary conservation and natural variance

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

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics

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

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

Proteochemometrics - recent developments in bioactivity and selectivity modeling