List of works - Chris de Graaf

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

scientific article (publication date: April 2016)

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

scientific article

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

scientific article published on 16 January 2018

7TM Domain Structure of Adhesion GPCRs

scientific article published on January 2016

A Molecular Pharmacologist's Guide to G Protein-Coupled Receptor Crystallography

scientific article

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

scientific article published in January 2018

A gold coordination compound as a chemical probe to unravel aquaporin-7 function

scientific article published on 28 May 2014

A medicinal chemistry perspective on melting point: matched molecular pair analysis of the effects of simple descriptors on the melting point of drug-like compounds

article

A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design

scientific article

Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors

scientific article

Advanced fluorescence microscopy reveals disruption of dynamic CXCR4 dimerization by subpocket-specific inverse agonists

scientific article published on 04 November 2020

Agonist-dependent effects of mutations in the sphingosine-1-phosphate type 1 receptor

Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study

scientific article published on 23 February 2007

Aminergic GPCR-ligand interactions: A chemical and structural map of receptor mutation data

scientific article published on 27 November 2018

Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs

scientific article published on 6 February 2015

Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

scientific article published in April 2005

Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy

scientific article published in February 2006

Bispyrimidines as potent histamine H(4) receptor ligands: delineation of structure-activity relationships and detailed H(4) receptor binding mode

scientific article

C(X)CR in silico: Computer-aided prediction of chemokine receptor-ligand interactions

scientific article published on January 2012

CXCR4-targeting nanobodies differentially inhibit CXCR4 function and HIV entry

Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking.

scientific article published in April 2006

Chemical subtleties in small-molecule modulation of peptide receptor function: the case of CXCR3 biaryl-type ligands

scientific article

Chemokine Receptor Crystal Structures: What Can Be Learned from Them?

scientific article published on 02 July 2019

Classification, Nomenclature, and Structural Aspects of Adhesion GPCRs

scientific article published on January 2016

Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT(3)A, Histamine H(1), and Histamine H(4) Receptors

scientific article published on 23 April 2015

Combining quantum mechanical ligand conformation analysis and protein modeling to elucidate GPCR-ligand binding modes

scientific article published on 19 November 2012

Conformational states of the full-length glucagon receptor

scientific article

Conformationally constrained opioid ligands: the Dmt-Aba and Dmt-Aia versus Dmt-Tic scaffold

scientific article

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

scientific article

Customizing G Protein-coupled receptor models for structure-based virtual screening

scientific article published on January 2009

Cytochrome p450 in silico: an integrative modeling approach.

scientific article

Design and pharmacological characterization of VUF14480, a covalent partial agonist that interacts with cysteine 98(3.36) of the human histamine H₄ receptor.

scientific article

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

scientific article

Diazepam-bound GABAA receptor models identify new benzodiazepine binding-site ligands

scientific article

Discovery of Novel Trypanosoma brucei Phosphodiesterase B1 Inhibitors by Virtual Screening against the Unliganded TbrPDEB1 Crystal Structure

scientific article

Dynamic tuneable G protein-coupled receptor monomer-dimer populations.

scientific article

Electron density fingerprints (EDprints): virtual screening using assembled information of electron density

scientific article published in October 2010

Erratum to: 7TM Domain Structure of Adhesion GPCRs.

scientific article

Estimation of kinetic parameter for the biotransformation of three-ring azaarenes by the phenanthrene-degrading strain Sphingomonas sp. LH128.

scientific article published in February 2004

Exploring the CXCR3 Chemokine Receptor with Small-Molecule Antagonists and Agonists

article

Extending the Structural View of Class B GPCRs.

scientific article

Fate modeling of nonylphenol ethoxylates and their metabolites in the Dutch Scheldt and Rhine estuaries: validation with new field data

article published in 2005

Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H₄ and the ion channel serotonin 5-HT₃A.

scientific article

Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations

scientific article published on 27 February 2007

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

scientific article

From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling

From three-dimensional GPCR structure to rational ligand discovery

scientific article published on January 2014

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

scientific article

Generic GPCR residue numbers - aligning topology maps while minding the gaps

scientific article

Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators

scientific article

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

scientific article

Identification of a novel allosteric binding site in the CXCR2 chemokine receptor

scientific article

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

scientific article

Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211.

scientific article published on 30 October 2013

Improved inhibition of the histone acetyltransferase PCAF by an anacardic acid derivative

scientific article published on 3 July 2010

In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions

Increasing selectivity of CC chemokine receptor 8 antagonists by engineering nondesolvation related interactions with the intended and off-target binding sites

scientific article

Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: crucial role in 7-methoxy-4-(aminomethyl)-coumarin metabolism

scientific article published in December 2004

Insights into the structure of class B GPCRs

scientific article

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

scientific article

KLIFS: a structural kinase-ligand interaction database

scientific article published on 22 October 2015

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

scientific article published on 21 October 2020

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

scientific article

Ligand efficiency as a guide in fragment hit selection and optimization

article published in 2010

Mapping histamine H4receptor–ligand binding modes

Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation.

scientific article

Metabolism ofN-substituted 7-methoxy-4-(aminomethyl) -coumarins by cytochrome P450 2D6 mutants and the indication of additional substrate interaction points

scientific article published on 01 September 2006

Molecular Modeling-Guided Site-Directed Mutagenesis of Cytochrome P450 2D6

article

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

scientific article published on 7 November 2011

Molecular determinants of ligand binding to H4R species variants

scientific article

Molecular determinants of selective agonist and antagonist binding to the histamine H₄ receptor

scientific article published on January 2011

Molecular interaction fingerprint approaches for GPCR drug discovery

scientific article

Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening

scientific article

Molecular pharmacology of histamine H4 receptors

scientific article published on June 2012

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

scientific article published on 23 February 2016

Pharmacological modulation of chemokine receptor function.

scientific article published on March 2012

Role of the conserved threonine 309 in mechanism of oxidation by cytochrome P450 2D6.

scientific article published on 21 October 2005

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

scientific article published on 05 July 2019

Selective Structure-Based Virtual Screening for Full and Partial Agonists of the β2 Adrenergic Receptor

Selective structure-based virtual screening for full and partial agonists of the beta2 adrenergic receptor

scientific article

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

scientific article

Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs

Structural Analysis of Chemokine Receptor-Ligand Interactions

scientific article

Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space

Structural Determinants of Binding the Seven-transmembrane Domain of the Glucagon-like Peptide-1 Receptor (GLP-1R)

scientific article

Structural insights into serotonin receptor ligands polypharmacology

scientific article published on 6 April 2018

Structure and Function of Peptide-Binding G Protein-Coupled Receptors

scientific article published on 10 July 2017

Structure of the full-length glucagon class B G-protein-coupled receptor

scientific article

Structure of the human glucagon class B G-protein-coupled receptor

scientific article

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

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

Structure‐Based Discovery of Allosteric Modulators of Two Related Class B G‐Protein‐Coupled Receptors ⬇️

scholarly article by Chris de Graaf et al published 12 October 2011 in ChemMedChem

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

scientific article published on 14 March 2018

Synthesis, biological evaluation, and automated docking of constrained analogues of the opioid peptide H-Dmt-D-Ala-Phe-Gly-NH₂ using the 4- or 5-methyl substituted 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one scaffold

scientific article published on 14 September 2011

Synthesis, modeling and functional activity of substituted styrene-amides as small-molecule CXCR7 agonists

scientific article published on 27 February 2012

Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.

scientific article published on 19 April 2018

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

scientific article

The receptor concept in 3D: from hypothesis and metaphor to GPCR-ligand structures

scientific article published on 08 August 2014

The role and application of in silico docking in chemical genomics research

scientific article published in January 2005

The role of phenylalanine 483 in cytochrome P450 2D6 is strongly substrate dependent

scientific article published in October 2005

Topological role of cytochrome P450 2D6 active site residues.

scientific article published on 23 January 2006

Triazole Ligands Reveal Distinct Molecular Features That Induce Histamine H4Receptor Affinity and Subtly Govern H4/H3Subtype Selectivity

scientific article published on 24 February 2011

Unnatural amino acids for the study of chemokine receptor structure and dynamics

Vanishing white matter: Eukaryotic initiation factor 2B model and the impact of missense mutations

scientific article published on 12 January 2021

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

scientific article published on 03 December 2012

List of works by Chris de Graaf

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

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

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

7TM Domain Structure of Adhesion GPCRs

A Molecular Pharmacologist's Guide to G Protein-Coupled Receptor Crystallography

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

A gold coordination compound as a chemical probe to unravel aquaporin-7 function

A medicinal chemistry perspective on melting point: matched molecular pair analysis of the effects of simple descriptors on the melting point of drug-like compounds

A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design

Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors

Advanced fluorescence microscopy reveals disruption of dynamic CXCR4 dimerization by subpocket-specific inverse agonists

Agonist-dependent effects of mutations in the sphingosine-1-phosphate type 1 receptor

Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study

Aminergic GPCR-ligand interactions: A chemical and structural map of receptor mutation data

Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs

Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy

Bispyrimidines as potent histamine H(4) receptor ligands: delineation of structure-activity relationships and detailed H(4) receptor binding mode

C(X)CR in silico: Computer-aided prediction of chemokine receptor-ligand interactions

CXCR4-targeting nanobodies differentially inhibit CXCR4 function and HIV entry

Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking.

Chemical subtleties in small-molecule modulation of peptide receptor function: the case of CXCR3 biaryl-type ligands

Chemokine Receptor Crystal Structures: What Can Be Learned from Them?

Classification, Nomenclature, and Structural Aspects of Adhesion GPCRs

Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT(3)A, Histamine H(1), and Histamine H(4) Receptors

Combining quantum mechanical ligand conformation analysis and protein modeling to elucidate GPCR-ligand binding modes

Conformational states of the full-length glucagon receptor

Conformationally constrained opioid ligands: the Dmt-Aba and Dmt-Aia versus Dmt-Tic scaffold

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

Customizing G Protein-coupled receptor models for structure-based virtual screening

Cytochrome p450 in silico: an integrative modeling approach.

Design and pharmacological characterization of VUF14480, a covalent partial agonist that interacts with cysteine 98(3.36) of the human histamine H₄ receptor.

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

Diazepam-bound GABAA receptor models identify new benzodiazepine binding-site ligands

Discovery of Novel Trypanosoma brucei Phosphodiesterase B1 Inhibitors by Virtual Screening against the Unliganded TbrPDEB1 Crystal Structure

Dynamic tuneable G protein-coupled receptor monomer-dimer populations.

Electron density fingerprints (EDprints): virtual screening using assembled information of electron density

Erratum to: 7TM Domain Structure of Adhesion GPCRs.

Estimation of kinetic parameter for the biotransformation of three-ring azaarenes by the phenanthrene-degrading strain Sphingomonas sp. LH128.

Exploring the CXCR3 Chemokine Receptor with Small-Molecule Antagonists and Agonists

Extending the Structural View of Class B GPCRs.

Fate modeling of nonylphenol ethoxylates and their metabolites in the Dutch Scheldt and Rhine estuaries: validation with new field data

Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H₄ and the ion channel serotonin 5-HT₃A.

Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations

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

From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling

From three-dimensional GPCR structure to rational ligand discovery

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

Generic GPCR residue numbers - aligning topology maps while minding the gaps

Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators

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

Identification of a novel allosteric binding site in the CXCR2 chemokine receptor

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

Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211.

Improved inhibition of the histone acetyltransferase PCAF by an anacardic acid derivative

In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions

Increasing selectivity of CC chemokine receptor 8 antagonists by engineering nondesolvation related interactions with the intended and off-target binding sites

Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: crucial role in 7-methoxy-4-(aminomethyl)-coumarin metabolism

Insights into the structure of class B GPCRs

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

KLIFS: a structural kinase-ligand interaction database

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

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

Ligand efficiency as a guide in fragment hit selection and optimization

Mapping histamine H4receptor–ligand binding modes

Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation.

Metabolism ofN-substituted 7-methoxy-4-(aminomethyl) -coumarins by cytochrome P450 2D6 mutants and the indication of additional substrate interaction points

Molecular Modeling-Guided Site-Directed Mutagenesis of Cytochrome P450 2D6

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

Molecular determinants of ligand binding to H4R species variants

Molecular determinants of selective agonist and antagonist binding to the histamine H₄ receptor

Molecular interaction fingerprint approaches for GPCR drug discovery

Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening

Molecular pharmacology of histamine H4 receptors

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

Pharmacological modulation of chemokine receptor function.

Role of the conserved threonine 309 in mechanism of oxidation by cytochrome P450 2D6.

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

Selective Structure-Based Virtual Screening for Full and Partial Agonists of the β2 Adrenergic Receptor