A. Kooistra

发表

Full combinatorial consensus scoring for ligand-based virtual fragment screening at membrane bound receptors

E. Haaksma, R. Leurs, S. Schultes, 2013 .

Kinase-Centric Computational Drug Development

Andrea Volkamer, A. Kooistra, 2017 .

KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space.

I. D. de Esch, R. Leurs, C. de Graaf, 2014, Journal of medicinal chemistry.

PDEStrIAn: A Phosphodiesterase Structure and Ligand Interaction Annotated Database As a Tool for Structure-Based Drug Design.

Georgi K. Kanev, I. D. de Esch, R. Leurs, 2016, Journal of medicinal chemistry.

Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data.

I. D. de Esch, R. Leurs, A. Bojarski, 2018, Journal of medicinal chemistry.

Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor.

R. Stevens, I. D. de Esch, R. Leurs, 2011, Journal of medicinal chemistry.

KLIFS : Knowledge ‐ based structural database to navigate kinase ‐ ligand interaction space Chapter 5

R. Leurs, A. Kooistra, O. V. Linden, 2013 .

Small and colorful stones make beautiful mosaics: fragment-based chemogenomics.

Saskia Nijmeijer, Chris de Graaf, Rob Leurs, 2013, Drug Discovery Today.

Small and Colorful Tesserae Make Beautiful Mosaics: Fragment‐based Chemogenomics Introduction

I. D. de Esch, R. Leurs, C. de Graaf, 2022 .

Chapter 6 Structure-based virtual fragment screening for ligands of the G protein-coupled histamine H 4 receptor

R. Smits, R. Leurs, H. Vischer, 2012 .

The Landscape of Atypical and Eukaryotic Protein Kinases.

Georgi K. Kanev, T. Wurdinger, I. D. de Esch, 2019, Trends in pharmacological sciences.

Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain

I. D. de Esch, C. de Graaf, A. J. Thompson, 2012, Bioorganic & medicinal chemistry.

A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design

R. Leurs, A. Kooistra, I. D. Esch, 2013, British journal of pharmacology.

The Receptor Concept in 3D: From Hypothesis and Metaphor to GPCR–Ligand Structures

C. de Graaf, H. Timmerman, A. Kooistra, 2014, Neurochemical Research.

Utilizing drug-target-event relationships to unveil safety patterns in pharmacovigilance

A. Hauser, A. Kooistra, M. Sessa, 2020, Expert opinion on drug safety.

Chemical Diversity in the G Protein-Coupled Receptor Superfamily.

R. Stevens, C. de Graaf, Ming-Wei Wang, 2018, Trends in pharmacological sciences.

KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome.

F. Rippmann, Andrea Volkamer, A. Kooistra, 2022, Journal of chemical information and modeling.

The Viral G Protein-Coupled Receptor ORF74 Hijacks β-Arrestins for Endocytic Trafficking in Response to Human Chemokines

R. Leurs, C. de Graaf, H. Vischer, 2015, PloS one.

Identification of Ligand Binding Hot Spots of the Histamine H1 Receptor following Structure-Based Fragment Optimization.

I. D. de Esch, R. Leurs, J. Mason, 2016, Journal of medicinal chemistry.

Structural insights into serotonin receptor ligands polypharmacology.

E. Lacivita, M. Leopoldo, A. Bojarski, 2018, European journal of medicinal chemistry.

KiSSim: Predicting off-targets from structural similarities in the kinome

F. Rippmann, Andrea Volkamer, A. Kooistra, 2021 .

Structure-Based Virtual Screening for Ligands of G Protein–CoupledReceptors: What CanMolecular DockingDo for You?

Jens Carlsson, F. Ballante, A. Kooistra, 2022 .

Differential GLP-1R binding and activation by peptide and non-peptide agonists

David E. Gloriam, C. Langmead, P. Sexton, 2020, bioRxiv.

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2).

I. D. de Esch, R. Leurs, M. Siderius, 2019, Bioorganic & medicinal chemistry.

Development of novel fluorescent histamine H1-receptor antagonists to study ligand-binding kinetics in living cells

Leigh A. Stoddart, R. Leurs, C. de Graaf, 2018, Scientific Reports.

Structure of the class D GPCR Ste2 dimer coupled to two G proteins

David E. Gloriam, N. Vaidehi, D. Gloriam, 2020, Nature.

Discovery of Diaryl Ether Substituted Tetrahydrophthalazinones as TbrPDEB1 Inhibitors Following Structure-Based Virtual Screening

I. D. de Esch, R. Leurs, M. Siderius, 2021, Frontiers in Chemistry.

In silico Medicinal Chemistry : Investigating GPCRs: key regulators of signal transduction and cell function

A. Kooistra, 2015 .

Structure-Based Virtual Screening for Ligands of G Protein–CoupledReceptors: What CanMolecular DockingDo for You?

Jens Carlsson, F. Ballante, A. Kooistra, 2022 .

GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources

David E. Gloriam, G. Keserü, D. Gloriam, 2022, Nucleic Acids Res..

An online GPCR structure analysis platform

David E. Gloriam, David Gloriam, Alexander Hauser, 2021, Nature Structural & Molecular Biology.

Covalent Inhibition of the Histamine H3 Receptor

I. D. de Esch, R. Leurs, G. Keserű, 2019, Molecules.

KLIFS: an overhaul after the first 5 years of supporting kinase research

Chris de Graaf, Iwan J. P. de Esch, Albert J. Kooistra, 2020, Nucleic Acids Res..

The G protein database, GproteinDb

David E. Gloriam, G. Keserü, A. Hauser, 2021, Nucleic Acids Res..

From heptahelical bundle to hits from the Haystack: structure-based virtual screening for GPCR ligands.

Chris de Graaf, Rob Leurs, Iwan J P de Esch, 2013, Methods in enzymology.

KLIFS: a structural kinase-ligand interaction database

Chris de Graaf, Iwan J. P. de Esch, Albert J. Kooistra, 2015, Nucleic Acids Res..

Molecular interaction fingerprint approaches for GPCR drug discovery.

Tina Ritschel, Márton Vass, Chris de Graaf, 2016, Current opinion in pharmacology.

Function-specific virtual screening for GPCR ligands using a combined scoring method

Chris de Graaf, Albert J. Kooistra, Rob Leurs, 2016, Scientific Reports.

The Landscape of Atypical and Eukaryotic Protein Kinases.

Georgi K. Kanev, I. D. de Esch, R. Leurs, 2019, Trends in pharmacological sciences.

GPCRdb in 2021: integrating GPCR sequence, structure and function

György M. Keserü, David E. Gloriam, Mauricio Esguerra, 2020, Nucleic Acids Res..

Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You?

C. de Graaf, Jens Carlsson, F. Ballante, 2021, Pharmacological Reviews.

GPCR activation mechanisms across classes and macro/microscales

M. Madan Babu, David E. Gloriam, David Gloriam, 2021, Nature Structural & Molecular Biology.

Uncovering patterns of atomic interactions in static and dynamic structures of proteins

A. J. Venkatakrishnan, M. Madan Babu, Ron O. Dror, 2019, bioRxiv.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Amir K. Foroushani, Yuanfang Guan, Jaewoo Kang, 2019, Nature Communications.

Mapping histamine H4 receptor–ligand binding modes

Saskia Nijmeijer, Chris de Graaf, Iwan J. P. de Esch, 2013 .

Chapter 6 Mapping histamine H 4 receptor – ligand binding modes

E. Haaksma, R. Leurs, H. Vischer, 2013 .

Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study

Chris de Graaf, Iwan J. P. de Esch, Albert J. Kooistra, 2015, J. Chem. Inf. Model..

Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists.

C. Langmead, P. Sexton, A. Christopoulos, 2020, Molecular cell.

A Structural Framework for GPCR Chemogenomics: What's In a Residue Number?

Stefan Verhoeven, Márton Vass, David E. Gloriam, 2018, Methods in molecular biology.

1.15 – Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space

Albert J. Kooistra, Georgi K. Kanev, I.J.P. de Esch, 2017 .

A community Biased Signaling Atlas

David E. Gloriam, A. Hauser, D. Gloriam, 2023, Nature Chemical Biology.

Structure of the class D GPCR Ste2 dimer coupled to two G proteins

N. Vaidehi, D. Gloriam, C. Tate, 2020, Nature.

Route to Prolonged Residence Time at the Histamine H1 Receptor: Growing from Desloratadine to Rupatadine

I. D. de Esch, R. Leurs, M. Waring, 2019, Journal of medicinal chemistry.

Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs

Andreas Bender, Oscar Méndez-Lucio, Albert J. Kooistra, 2015, J. Chem. Inf. Model..

Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT3A, Histamine H1, and Histamine H4 Receptors

Saskia Nijmeijer, Chris de Graaf, Iwan J. P. de Esch, 2015, J. Chem. Inf. Model..

Chapter 5 Molecular determinants of ligand binding modes in the histamine H 4 receptor : Linking ligand-based 3 D-QSAR models to in silico guided receptor mutagenesis studies Adapted from :

H. Vischer, A. Kooistra, L. Roumen, 2012 .

3D‐e‐Chem: Structural Cheminformatics Workflows for Computer‐Aided Drug Discovery

Stefan Verhoeven, Ross McGuire, Márton Vass, 2018, ChemMedChem.

Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies.

Saskia Nijmeijer, Chris de Graaf, Rob Leurs, 2011, Journal of medicinal chemistry.

Structure-Based Virtual Screening for Ligands of G Protein–CoupledReceptors: What CanMolecular DockingDo for You?

Jens Carlsson, F. Ballante, A. Kooistra, 2022 .

The Receptor Concept in 3D: From Hypothesis and Metaphor to GPCR–Ligand Structures

H. Timmerman, A. Kooistra, C. Graaf, 2014, Neurochemical Research.

3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

Lars Ridder, Chris de Graaf, Tina Ritschel, 2017, J. Chem. Inf. Model..

Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4 receptor

Saskia Nijmeijer, Chris de Graaf, Iwan J. P. de Esch, 2015 .

From three-dimensional GPCR structure to rational ligand discovery.

Chris de Graaf, Rob Leurs, Iwan J P de Esch, 2014, Advances in experimental medicine and biology.

Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints

Saskia Nijmeijer, Chris de Graaf, Albert J. Kooistra, 2012, J. Chem. Inf. Model..

Synthesis and Characterization of a Bidirectional Photoswitchable Antagonist Toolbox for Real-Time GPCR Photopharmacology

Rob Leurs, Iwan J P de Esch, Albert J Kooistra, 2018, Journal of the American Chemical Society.

Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure.

Chris de Graaf, Rob Leurs, Iwan J P de Esch, 2013, Journal of medicinal chemistry.

Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks

Georgi K. Kanev, I. D. de Esch, C. de Graaf, 2023, PLoS Comput. Biol..

Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density

Jaap Heringa, Chris de Graaf, Johannes H. G. M. van Beek, 2010, J. Chem. Inf. Model..

Structural insights into serotonin receptor ligands polypharmacology.

E. Lacivita, M. Leopoldo, A. Bojarski, 2018, European journal of medicinal chemistry.

From heptahelical bundle to hits from the Haystack: structure-based virtual screening for GPCR ligands.

I. D. de Esch, R. Leurs, C. de Graaf, 2013, Methods in enzymology.

Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure.

H. Ke, I. D. de Esch, R. Leurs, 2013, Journal of medicinal chemistry.

PGxDB: an interactive web-platform for pharmacogenomics research.

David E. Gloriam, A. Kooistra, Ziaurrehman Tanoli, 2024, Nucleic acids research.