List of works - Didier Rognan

5(th) Strasbourg Summer School in Chemoinformatics

scientific article

A Summer School for Structuring the Chemoinformatics Community

scientific article published in June 2014

A simple and fuzzy method to align and compare druggable ligand-binding sites

scientific article published in June 2008

A step-economical multicomponent synthesis of 3D-shaped aza-diketopiperazines and their drug-like chemical space analysis

scientific article published in September 2016

A three-dimensional model of the neprilysin 2 active site based on the X-ray structure of neprilysin. Identification of residues involved in substrate hydrolysis and inhibitor binding of neprilysin 2

scientific journal article

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

Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites

scientific article published in January 2010

All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening

scientific article published on 04 January 2019

Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5).

scientific article

Assessing the scaffold diversity of screening libraries

scientific article published in March 2006

Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement

scientific article published on 19 June 2020

Beware of machine learning-based scoring functions-on the danger of developing black boxes

scientific article

Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements

scientific article

Binding properties of pyochelin and structurally related molecules to FptA of Pseudomonas aeruginosa

scientific article published on 8 February 2006

Chemical databases and virtual screening

scientific article

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

scientific article published in November 2004

Comparing atom-based with residue-based descriptors in predicting binding site similarity: do backbone atoms matter?

scientific article published on 15 September 2016

Computational profiling of bioactive compounds using a target-dependent composite workflow

scientific article published on 26 August 2013

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

scientific article

ConsDock: A new program for the consensus analysis of protein-ligand interactions

scientific article

Correction: Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements.

scientific article

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

scientific article published on January 2009

Delineating a Ca2+ binding pocket within the venus flytrap module of the human calcium-sensing receptor

scientific article

Design of a general-purpose European compound screening library for EU-OPENSCREEN.

scientific article published on 15 July 2014

Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands.

scientific article

Development and virtual screening of target libraries

scientific article published on 3 February 2006

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.

scientific article published on August 2016

Domain versatility in plant AB-toxins: evidence for a local, pH-dependent rearrangement in the 2gamma lectin site of the mistletoe lectin by applying ligand derivatives and modelling

scientific article published on 2 June 2008

Encoding protein-ligand interaction patterns in fingerprints and graphs

scientific article published on 6 March 2013

Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel ⬇️

scientific article published on June 21, 2011

Estrogen receptor alpha as a key target of red wine polyphenols action on the endothelium.

scientific article

Exhaustive Repertoire of Druggable Cavities at Protein–Protein Interfaces of Known Three-Dimensional Structure

scientific article published on 25 October 2019

Fragment-Based Approaches and Computer-Aided Drug Discovery ⬇️

scientific article published on January 1, 2012

Functional characterization of sonic hedgehog mutations associated with holoprosencephaly

scientific article published on 28 July 2004

Glucose 6P binds and activates HlyIIR to repress Bacillus cereus haemolysin hlyII gene expression

scientific article

High-throughput modeling of human G-protein coupled receptors: amino acid sequence alignment, three-dimensional model building, and receptor library screening

scientific article

Hot-spots-guided receptor-based pharmacophores (HS-Pharm): a knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores

scientific article published on 21 June 2008

IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein-Ligand Interactions

scientific article

Identification and characterisation of the dopamine receptor II from the cat flea Ctenocephalides felis (CfDopRII).

scientific article published on 7 August 2006

Identification by high-throughput screening of inhibitors of Schistosoma mansoni NAD(+) catabolizing enzyme

scientific article

Identification of nonpeptide CCR5 receptor agonists by structure-based virtual screening

scientific article

Identification of the binding sites of the SR49059 nonpeptide antagonist into the V1a vasopressin receptor using sulfydryl-reactive ligands and cysteine mutants as chemical sensors

scientific article (publication date: 10 October 2003)

In silico-guided target identification of a scaffold-focused library: 1,3,5-triazepan-2,6-diones as novel phospholipase A2 inhibitors

scientific article

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

scientific article

LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening

scientific article published on 13 April 2020

Lead Identification by Virtual Screening

Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses

scientific article published on 18 July 2019

Mapping the binding site of arginine vasopressin to V1a and V1b vasopressin receptors

scientific article published on 2 November 2006

Modeling and Mutagenesis of the Binding Site of Calhex 231, a Novel Negative Allosteric Modulator of the Extracellular Ca2+-sensing Receptor ⬇️

scientific article published on September 23, 2003

Molecular determinants of non-competitive antagonist binding to the mouse GPRC6A receptor

scientific article published on November 2009

Molecular mimicry of an HLA-B27-derived ligand of arthritis-linked subtypes with chlamydial proteins

scientific article published on 16 July 2002

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

scientific article

N,N'-linked oligoureas as foldamers: chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics

scientific article published in February 2005

N1-Benzoyl-N2-[1-(1-naphthyl)ethyl]-trans-1,2-diaminocyclohexanes: Development of 4-chlorophenylcarboxamide (calhex 231) as a new calcium sensing receptor ligand demonstrating potent calcilytic activity

scientific article

Novel aminotetrazole derivatives as selective STAT3 non-peptide inhibitors

scientific article published on September 2015

Optimizing fragment and scaffold docking by use of molecular interaction fingerprints

scientific article published in January 2007

Positive and negative allosteric modulators of the Ca2+-sensing receptor interact within overlapping but not identical binding sites in the transmembrane domain

scientific article published on 19 February 2004

Predicting ligand binding modes from neural networks trained on protein-ligand interaction fingerprints

scientific article published on 29 March 2013

Probing the cysteine-34 position of endogenous serum albumin with thiol-binding doxorubicin derivatives. Improved efficacy of an acid-sensitive doxorubicin derivative with specific albumin-binding properties compared to that of the parent compound

scientific article published in December 2002

Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets?

scientific article published in January 2003

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling ⬇️

scientific article published on April 11, 2012

Proteome-scale docking: myth and reality

scientific article

Pyochelin Enantiomers and Their Outer-Membrane Siderophore Transporters in Fluorescent Pseudomonads: Structural Bases for Unique Enantiospecific Recognition ⬇️

scientific article published on September 23, 2011

Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.

scientific article

Ranking targets in structure-based virtual screening of three-dimensional protein libraries: methods and problems

scientific article

Recovering the true targets of specific ligands by virtual screening of the protein data bank

scientific article

Redesign of Schistosoma mansoni NAD+ catabolizing enzyme: active site H103W mutation restores ADP-ribosyl cyclase activity

scientific article published on October 2006

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

Stable helical secondary structure in short-chain N,N'-linked oligoureas bearing proteinogenic side chains

scientific article published in June 2002

Stereospecificity of the siderophore pyochelin outer membrane transporters in fluorescent pseudomonads

scientific article published on 17 March 2009

Structural insights into the molecular basis of the ligand promiscuity

scientific article published on 5 September 2012

Structure-Based Approaches to Target Fishing and Ligand Profiling

scientific article

Structure-Based Detection of Orthosteric and Allosteric Pockets at Protein-Protein Interfaces

scientific article published on 01 January 2018

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 biological properties of thiazole-analogues of pyochelin, a siderophore of Pseudomonas aeruginosa

scientific article published on 4 December 2013

Synthesis of (+/-)-2-O-[4'-(N-9''-purinyl)butyl] myo-inositol 1,4,5-tris(phosphate), a potent full agonist at the D-myo-inositol 1,4,5-tris(phosphate) receptor.

scientific article published on February 2005

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

Targeting of Smoothened for therapeutic gain

scientific article published on April 2014

The impact of in silico screening in the discovery of novel and safer drug candidates

scientific article

Topological analysis of the complex formed between neurokinin A and the NK2 tachykinin receptor

scientific article published on April 2007

Unsupervised Classification of G-Protein Coupled Receptors and Their Conformational States Using IChem Intramolecular Interaction Patterns

scientific article published on 29 August 2019

Ureidopeptide GLP-1 analogues with prolonged activity in vivo via signal bias and altered receptor trafficking

scientific article published on 11 September 2019

[Structure of the Smoothened receptor].

scientific article

sc-PDB: a 3D-database of ligandable binding sites--10 years on

scientific article

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins

scientific article

sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank

scientific article

List of works by Didier Rognan

5(th) Strasbourg Summer School in Chemoinformatics

A Summer School for Structuring the Chemoinformatics Community

A simple and fuzzy method to align and compare druggable ligand-binding sites

A step-economical multicomponent synthesis of 3D-shaped aza-diketopiperazines and their drug-like chemical space analysis

A three-dimensional model of the neprilysin 2 active site based on the X-ray structure of neprilysin. Identification of residues involved in substrate hydrolysis and inhibitor binding of neprilysin 2

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

Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites

All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening

Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5).

Assessing the scaffold diversity of screening libraries

Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement

Beware of machine learning-based scoring functions-on the danger of developing black boxes

Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements

Binding properties of pyochelin and structurally related molecules to FptA of Pseudomonas aeruginosa

Chemical databases and virtual screening

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

Comparing atom-based with residue-based descriptors in predicting binding site similarity: do backbone atoms matter?

Computational profiling of bioactive compounds using a target-dependent composite workflow

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

ConsDock: A new program for the consensus analysis of protein-ligand interactions

Correction: Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements.

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

Delineating a Ca2+ binding pocket within the venus flytrap module of the human calcium-sensing receptor

Design of a general-purpose European compound screening library for EU-OPENSCREEN.

Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands.

Development and virtual screening of target libraries

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.

Domain versatility in plant AB-toxins: evidence for a local, pH-dependent rearrangement in the 2gamma lectin site of the mistletoe lectin by applying ligand derivatives and modelling

Encoding protein-ligand interaction patterns in fingerprints and graphs

Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel ⬇️

Estrogen receptor alpha as a key target of red wine polyphenols action on the endothelium.

Exhaustive Repertoire of Druggable Cavities at Protein–Protein Interfaces of Known Three-Dimensional Structure

Fragment-Based Approaches and Computer-Aided Drug Discovery ⬇️

Functional characterization of sonic hedgehog mutations associated with holoprosencephaly

Glucose 6P binds and activates HlyIIR to repress Bacillus cereus haemolysin hlyII gene expression

High-throughput modeling of human G-protein coupled receptors: amino acid sequence alignment, three-dimensional model building, and receptor library screening

Hot-spots-guided receptor-based pharmacophores (HS-Pharm): a knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores

IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein-Ligand Interactions

Identification and characterisation of the dopamine receptor II from the cat flea Ctenocephalides felis (CfDopRII).

Identification by high-throughput screening of inhibitors of Schistosoma mansoni NAD(+) catabolizing enzyme

Identification of nonpeptide CCR5 receptor agonists by structure-based virtual screening

Identification of the binding sites of the SR49059 nonpeptide antagonist into the V1a vasopressin receptor using sulfydryl-reactive ligands and cysteine mutants as chemical sensors

In silico-guided target identification of a scaffold-focused library: 1,3,5-triazepan-2,6-diones as novel phospholipase A2 inhibitors

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

LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening

Lead Identification by Virtual Screening

Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses

Mapping the binding site of arginine vasopressin to V1a and V1b vasopressin receptors

Modeling and Mutagenesis of the Binding Site of Calhex 231, a Novel Negative Allosteric Modulator of the Extracellular Ca2+-sensing Receptor ⬇️

Molecular determinants of non-competitive antagonist binding to the mouse GPRC6A receptor

Molecular mimicry of an HLA-B27-derived ligand of arthritis-linked subtypes with chlamydial proteins

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

N,N'-linked oligoureas as foldamers: chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics

N1-Benzoyl-N2-[1-(1-naphthyl)ethyl]-trans-1,2-diaminocyclohexanes: Development of 4-chlorophenylcarboxamide (calhex 231) as a new calcium sensing receptor ligand demonstrating potent calcilytic activity

Novel aminotetrazole derivatives as selective STAT3 non-peptide inhibitors

Optimizing fragment and scaffold docking by use of molecular interaction fingerprints

Positive and negative allosteric modulators of the Ca2+-sensing receptor interact within overlapping but not identical binding sites in the transmembrane domain

Predicting ligand binding modes from neural networks trained on protein-ligand interaction fingerprints

Probing the cysteine-34 position of endogenous serum albumin with thiol-binding doxorubicin derivatives. Improved efficacy of an acid-sensitive doxorubicin derivative with specific albumin-binding properties compared to that of the parent compound

Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets?

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling ⬇️

Proteome-scale docking: myth and reality

Pyochelin Enantiomers and Their Outer-Membrane Siderophore Transporters in Fluorescent Pseudomonads: Structural Bases for Unique Enantiospecific Recognition ⬇️

Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.

Ranking targets in structure-based virtual screening of three-dimensional protein libraries: methods and problems

Recovering the true targets of specific ligands by virtual screening of the protein data bank

Redesign of Schistosoma mansoni NAD+ catabolizing enzyme: active site H103W mutation restores ADP-ribosyl cyclase activity

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

Stable helical secondary structure in short-chain N,N'-linked oligoureas bearing proteinogenic side chains

Stereospecificity of the siderophore pyochelin outer membrane transporters in fluorescent pseudomonads

Structural insights into the molecular basis of the ligand promiscuity

Structure-Based Approaches to Target Fishing and Ligand Profiling

Structure-Based Detection of Orthosteric and Allosteric Pockets at Protein-Protein Interfaces

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

Synthesis and biological properties of thiazole-analogues of pyochelin, a siderophore of Pseudomonas aeruginosa

Synthesis of (+/-)-2-O-[4'-(N-9''-purinyl)butyl] myo-inositol 1,4,5-tris(phosphate), a potent full agonist at the D-myo-inositol 1,4,5-tris(phosphate) receptor.

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

Targeting of Smoothened for therapeutic gain