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List of works by Jean-Louis Reymond

"Ring Breaker": Neural Network Driven Synthesis Prediction of the Ring System Chemical Space

scientific article published on 30 April 2020

"Social" network of isomers based on bond count distance: algorithms

scientific article published on 13 January 2014

3-(aminomethyl)piperazine-2,5-dione as a novel NMDA glycine site inhibitor from the chemical universe database GDB.

scientific article published on 10 April 2009

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13

scientific article (publication date: July 2009)

A Glycopeptide Dendrimer Inhibitor of the Galactose-Specific Lectin LecA and of Pseudomonas aeruginosa Biofilms

scientific article

A Potent and Selective Janus Kinase Inhibitor with a Chiral 3D-Shaped Triquinazine Ring System from Chemical Space

scientific article published on 28 September 2020

A Probabilistic Molecular Fingerprint for Big Data Settings

A catalytically essential motif in external loop 5 of the bacterial oligosaccharyltransferase PglB

scientific article

A combinatorial approach to catalytic peptide dendrimers

scientific article

A cyclodecapeptide ligand to vitamin B12.

scientific article published on 16 September 2008

A general method for designing combinatorial peptide libraries decodable by amino acid analysis

scientific article

A green fluorescent chemosensor for amino acids provides a versatile high-throughput screening (HTS) assay for proteases

scientific article published on 01 May 2003

A multi-fingerprint browser for the ZINC database

scientific article

A peptide dendrimer enzyme model with a single catalytic site at the core

scientific article

A peptide dendrimer model for vitamin B12 transport proteins

scientific article

A probabilistic molecular fingerprint for big data settings

scientific article published on 18 December 2018

A searchable map of PubChem

scientific article

A strong positive dendritic effect in a peptide dendrimer-catalyzed ester hydrolysis reaction

scientific article published in December 2004

Adaptive and Mutational Responses to Peptide Dendrimer Antimicrobials in Pseudomonas aeruginosa

scientific article published on 24 March 2020

AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning

scientific article published on 17 November 2020

Aldehyde detection by chromogenic/fluorogenic oxime bond fragmentation

scientific article

An Enzyme Assay Using pM This work was supported by the Swiss National Science Foundation and the University of Bern

scientific article published on 01 May 2001

An antimicrobial bicyclic peptide from chemical space against multidrug resistant Gram-negative bacteria

scientific article published in May 2018

Analytical chemistry: a dendritic signal amplifier.

scientific article

Artificial aldolases from peptide dendrimer combinatorial libraries

scientific article

Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning

scientific article published on 28 September 2020

Atom pair 2D-fingerprints perceive 3D-molecular shape and pharmacophores for very fast virtual screening of ZINC and GDB-17.

scientific article

BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry

scientific article

Bead diffusion assay for discovering antimicrobial cyclic peptides

scientific article

Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability.

scientific article

CH-π "T-shape" interaction with histidine explains binding of aromatic galactosides to Pseudomonas aeruginosa lectin LecA

scientific article

Carbohydrate Transformer: Predicting Regio- and Stereoselective Reactions Using Transfer Learning

Carbohydrate Transformer: Predicting Regio- and Stereoselective Reactions Using Transfer Learning

scientific article

Catalytic peptide dendrimers

scientific article published on 01 March 2003

ChEMBL-Likeness Score and Database GDBChEMBL

scientific article published on 04 February 2020

Characterization of the single-subunit oligosaccharyltransferase STT3A from Trypanosoma brucei using synthetic peptides and lipid-linked oligosaccharide analogs

scientific article

Chemical Space: Big Data Challenge for Molecular Diversity

scientific article

Chemical space as a source for new drugs

scientific article published in 2010

Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms.

scientific article published on 13 July 2017

Chemical space travel

scientific article published on 01 May 2007

Chemo-enzymatic synthesis of lipid-linked GlcNAc2Man5 oligosaccharides using recombinant Alg1, Alg2 and Alg11 proteins

scientific article published in June 2017

Classification of organic molecules by molecular quantum numbers

scientific article published on 01 November 2009

Classifying enzymes from selectivity fingerprints

scientific article published in June 2004

Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning

scientific article published in 2021

Cluster analysis of the DrugBank chemical space using molecular quantum numbers

scientific article published on 14 March 2012

Combinatorial discovery of peptide dendrimer enzyme models hydrolyzing isobutyryl fluorescein

scientific article

Combinatorial libraries of peptide dendrimers: design, synthesis, on-bead high-throughput screening, bead decoding and characterization

scientific article

Combinatorial synthesis, selection, and properties of esterase peptide dendrimers

scientific article published in January 2006

Combining topology and sequence design for the discovery of potent antimicrobial peptide dendrimers against multidrug-resistant Pseudomonas aeruginosa

scientific article published on 24 October 2014

Comparing dendritic with linear esterase peptides by screening SPOT arrays for catalysis

scientific article

Convergent synthesis and cellular uptake of multivalent cell penetrating peptides derived from Tat, Antp, pVEC, TP10 and SAP.

scientific article published on 9 August 2013

Corrigendum: Anti-Microbial Dendrimers against Multidrug-Resistant P. aeruginosa Enhance the Angiogenic Effect of Biological Burn-wound Bandages

scientific article published on 7 April 2016

Data augmentation strategies to improve reaction yield predictions and estimate uncertainty

Data-Driven Chemical Reaction Classification, Fingerprinting and Clustering using Attention-Based Neural Networks

Data-Driven Chemical Reaction Classification, Fingerprinting and Clustering using Attention-Based Neural Networks

scientific article

Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain

scientific article published on 05 November 2019

Deep Learning Invades Drug Design and Synthesis

scientific article published in February 2018

Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa

scientific article published on 4 September 2017

Designed cell penetrating peptide dendrimers efficiently internalize cargo into cells

scientific article published on 01 July 2014

Discovery and characterization of a novel non-competitive inhibitor of the divalent metal transporter DMT1/SLC11A2.

scientific article published on 3 June 2015

Discovery of NMDA glycine site inhibitors from the chemical universe database GDB.

scientific article

Discovery of a Selective Aurora A Kinase Inhibitor by Virtual Screening

scientific article

Discovery of new peptide-based catalysts for the direct asymmetric aldol reaction

scientific article

Discovery of potent positive allosteric modulators of the α3β2 nicotinic acetylcholine receptor by a chemical space walk in ChEMBL.

scientific article

Discovery of α7-nicotinic receptor ligands by virtual screening of the chemical universe database GDB-13.

scientific article

Drug Analogs from Fragment Based Long Short-Term Memory Generative Neural Networks

Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks

scientific article published on 08 April 2019

Dual mechanism of zinc-proline catalyzed aldol reactions in water

scientific article published on 02 March 2006

Efficient Transfection of siRNA by Peptide Dendrimer-Lipid Conjugates.

scientific article published on 9 November 2016

Electrostatics and flexibility drive membrane recognition and early penetration by the antimicrobial peptide dendrimer bH1.

scientific article

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17.

scientific article

Enzyme Fingerprints by Fluorogenic and Chromogenic Substrate Arrays We would like to thank Prof. R. Furstoss and Dr. A. Archelas at the Faculté des Sciences de Luminy, Marseille, France, for providing a sample of Aspergillus niger EH, and Dr. C. Wei

scientific article published in December 2001

Enzyme activity fingerprinting with substrate cocktails

scientific article published on 01 September 2004

Enzyme assay and activity fingerprinting of hydrolases with the red-chromogenic adrenaline test

scientific article

Enzyme assays

scientific article published on 17 October 2008

Enzyme assays for high-throughput screening

scientific article published in August 2004

Enzyme fingerprints of activity, and stereo- and enantioselectivity from fluorogenic and chromogenic substrate arrays

scientific article published on 01 July 2002

Expanding the accessible chemical space by solid phase synthesis of bicyclic homodetic peptides

scientific article published on 27 October 2011

Expanding the fragrance chemical space for virtual screening

scientific article

Expanding the topological space of bioactive peptides

scientific article published on January 2013

Exploring Chemical Space with Machine Learning

scientific article published on 01 December 2019

Exploring DrugBank in Virtual Reality Chemical Space

scientific article published on 24 August 2018

Exploring Drugbank in Virtual Reality Chemical Space

Exploring chemical space for drug discovery using the chemical universe database

scientific article

Exploring the GDB-13 Chemical Space Using Deep Generative Models

Exploring the GDB-13 chemical space using deep generative models

article by Josep Arús-Pous et al published 12 March 2019 in Journal of Cheminformatics

Exploring the chemical space of known and unknown organic small molecules at www.gdb.unibe.ch

scientific article published on January 2011

Exploring α7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB

scientific article

Extraction of organic chemistry grammar from unsupervised learning of chemical reactions

FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web.

scientific article published on 24 November 2017

Five-substrate cocktail as a sensor array for measuring enzyme activity fingerprints of lipases and esterases

scientific article published on 18 January 2011

Fluorescence Imaging of Bacterial Killing by Antimicrobial Peptide Dendrimer G3KL

scientific article published on 31 October 2019

Fluorogenic stereochemical probes for transaldolases

scientific article published in February 2003

Fragment Database FDB-17.

scientific article published on 4 April 2017

Frontiers in Medicinal Chemistry 2017 in Bern, Switzerland.

scientific article published on 22 September 2017

Future turnovers in enzyme catalysis

scientific article published on 19 March 2010

Glycocluster Tetrahydroxamic Acids Exhibiting Unprecedented Inhibition of Pseudomonas aeruginosa Biofilms

scientific article published on 26 August 2019

Glycopeptide dendrimer colchicine conjugates targeting cancer cells

scientific article

Glycopeptide dendrimers as Pseudomonas aeruginosa biofilm inhibitors

scientific article

Glycopeptide dendrimers with high affinity for the fucose-binding lectin LecB from Pseudomonas aeruginosa

scientific article

Glycopeptide dendrimers: tuning carbohydrate-lectin interactions with amino acids

scientific article published on 01 November 2010

Identification of catalytic Peptide dendrimers by "off-bead" in silica high-throughput screening of combinatorial libraries

scientific article

Identification of potent and selective small molecule inhibitors of the cation channel TRPM4.

scientific article published on 26 March 2018

Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB).

scientific article

Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT-β) as the Target of a Nanomolar Angiogenesis Inhibitor from a Phenotypic Screen Using the Polypharmacology Browser PPB2

scientific article published on 06 December 2018

Improved fluorescence assays to measure the defects associated with F508del-CFTR allow identification of new active compounds

scientific article

In Vitro Activity of the Novel Antimicrobial Peptide Dendrimer G3KL against Multidrug-Resistant Acinetobacter baumannii and Pseudomonas aeruginosa

scientific article

Inactivation-mimicking block of the epithelial calcium channel TRPV6

scientific article published on 27 November 2020

Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB

scientific article

Inhibition of mitosis by glycopeptide dendrimer conjugates of colchicine

scientific article

Iterative Oxime Bond Chemistry Leads to Protease Inhibitors

scientific article published on 01 November 2003

Lipidated Peptide Dendrimers Killing Multidrug-Resistant Bacteria.

scientific article

MQN-mapplet: visualization of chemical space with interactive maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13.

scientific article

Machine learning designs non-hemolytic antimicrobial peptides

scientific article published on 07 June 2021

Mapping of the Available Chemical Space versus the Chemical Universe of Lead-like Compounds

scientific article published on 20 November 2017

Mapping the Azolog Space Enables the Optical Control of New Biological Targets

scientific article published on 13 March 2019

Mapping the Space of Chemical Reactions using Attention-Based Neural Networks

Mapping the space of chemical reactions using attention-based neural networks

Mechanism of bacterial oligosaccharyltransferase: in vitro quantification of sequon binding and catalysis

scientific article published on 4 February 2013

Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds

scientific article published on 5 December 2019

Medicinal Chemistry Aware Database GDBMedChem

Medicinal Chemistry Database GDBMedChem

scientific article published on 27 February 2019

Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits.

scientific article published on 16 August 2017

Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase.

scientific article

Multivalency effects on Pseudomonas aeruginosa biofilm inhibition and dispersal by glycopeptide dendrimers targeting lectin LecA

scientific article

Multivalent glycoconjugates as anti-pathogenic agents ⬇️

scientific article

Neoglycopeptide dendrimer libraries as a source of lectin binding ligands

scientific article

Novel Peptide-dendrimer/Lipid/Oligonucleotide Ternary Complexes for Efficient Cellular Uptake and Improved Splice-Switching Activity

scientific article published on 04 September 2018

OMA & OPA - A Software Tool for Mass Spectrometric Sequencing of Nucleic Acids.

scientific article published in February 2014

OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids ⬇️

scientific article published on December 21, 2012

One Molecular Fingerprint to Rule them All: Drugs, Biomolecules, and the Metabolome

One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome

Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand-Based Virtual Screening Method

scientific article published on 12 October 2015

Optimizing Antimicrobial Peptide Dendrimers in Chemical Space

scientific article published on 15 June 2018

Optimizing TRPM4 inhibitors in the MHFP6 chemical space

scientific article published on 24 January 2019

Overcoming antibiotic resistance in Pseudomonas aeruginosa biofilms using glycopeptide dendrimers.

scientific article

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

scientific article

Peptide Dendrimer-Lipid Conjugates as DNA and siRNA Transfection Reagents: Role of Charge Distribution Across Generations

scientific article published in April 2017

Peptide and glycopeptide dendrimer apple trees as enzyme models and for biomedical applications

scientific article

Peptide dendrimer enzyme models for ester hydrolysis and aldolization prepared by convergent thioether ligation

scientific article published on 30 August 2011

Peptide dendrimer/lipid hybrid systems are efficient DNA transfection reagents: structure--activity relationships highlight the role of charge distribution across dendrimer generations

scientific article published on 17 May 2013

Peptide dendrimers G3KL and TNS18 inhibit Pseudomonas aeruginosa biofilms

scientific article published on 17 May 2019

Phenolic oxime oligomers inhibit Alzheimer's amyloid fibril formation and disaggregate fibrils in vitro

scientific article

Photoswitchable Inhibitor of the Calcium Channel TRPV6

scientific article published on 02 August 2019

Physiological and Molecular Function of the Sodium/Hydrogen Exchanger NHA2 (SLC9B2)

scientific article published on 21 December 2022

Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning

scientific article published on 31 December 2018

Populating Chemical Space with Peptides Using a Genetic Algorithm

scientific article published on 07 January 2020

Populating Chemical Space with Peptides using a Genetic Algorithm

Prebiotic carbohydrate synthesis: zinc-proline catalyzes direct aqueous aldol reactions of alpha-hydroxy aldehydes and ketones

scientific article published on 14 April 2005

Predicting Enzymatic Reactions with a Molecular Transformer

Predicting Enzymatic Reactions with a Molecular Transformer

Predicting Enzymatic Reactions with a Molecular Transformer

Predicting enzymatic reactions with a molecular transformer

Prediction of Chemical Reaction Yields using Deep Learning

scholarly article published 5 August 2020

Prediction of Chemical Reaction Yields using Deep Learning

scientific article

Prediction of Chemical Reaction Yields using Deep Learning

scholarly article published 12 October 2020

Prediction of chemical reaction yields using deep learning

scholarly article by Philippe Schwaller et al published 1 March 2021 in Machine Learning Science and Technology

Proteolysis of peptide dendrimers

scientific article

PubChem and ChEMBL Beyond Lipinski

scientific article published on 15 February 2019

PubChem and ChEMBL beyond Lipinski

scientific article published on 07 March 2019

Randomized SMILES Strings Improve the Quality of Molecular Generative Models

Randomized SMILES strings improve the quality of molecular generative models

article published in 2019

Reaction classification and yield prediction using the differential reaction fingerprint DRFP

scientific article published in January 2022

Recent advances in enzyme assays

scientific article

Remote control of bipyridine-metal coordination within a peptide dendrimer

scientific article published on 2 September 2009

SMILES-Based Deep Generative Scaffold Decorator for De-Novo Drug Design

SMILES-based deep generative scaffold decorator for de-novo drug design

scientific article published on 29 May 2020

SMIfp (SMILES fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules

scientific article

Selective catalysis with peptide dendrimers

scientific article

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

scientific article published on 24 July 2015

SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript

scientific article published on 19 December 2017

Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection

scientific article published on 09 August 2019

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

scientific article (publication date: 2015)

Structural Insight into Multivalent Galactoside Binding to Pseudomonas aeruginosa Lectin LecA

scientific article

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.

scientific article published on 31 January 2018

Structure and binding of peptide-dendrimer ligands to vitamin B12.

scientific article published in February 2010

Structure and mechanism of an active lipid-linked oligosaccharide flippase

scientific article

Structure and mechanism of the ER-based glucosyltransferase ALG6

scientific article published on 26 February 2020

Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide

scientific article published in Scientific Reports

Structure-activity relationships in aminocyclopentitol glycosidase inhibitors

scientific article published on 19 March 2004

Structure-based optimization of the terminal tripeptide in glycopeptide dendrimer inhibitors of Pseudomonas aeruginosa biofilms targeting LecA

scientific article

Substrate arrays as enzyme fingerprinting tools

scientific article

Substrate specificity of cytoplasmic N-glycosyltransferase

scientific article

Synergistic Effect of Propidium Iodide and Small Molecule Antibiotics with the Antimicrobial Peptide Dendrimer G3KL against Gram-Negative Bacteria

scientific article published on 30 November 2020

Synthesis and Nicotinic Receptor Activity of Chemical Space Analogues of N-(3R)-1-Azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) and 1,4-Diazabicyclo[3.2.2]nonane-4-carboxylic Acid 4-Bromophenyl Ester (SSR180711) ⬇️

scientific article published on May 16, 2012

Synthesis and activity of histidine-containing catalytic peptide dendrimers

scientific article published on 01 June 2006

Synthesis and esterolytic activity of catalytic peptide dendrimers

scientific article published in March 2004

Synthesis of ether oligomers.

scientific article

Synthesis of glycopeptide dendrimers, dimerization and affinity for Concanavalin A ⬇️

scientific article published on 08 April 2011

The Chemical Space Project

scientific article (publication date: 17 March 2015)

The Generated Databases (GDBs) as a Source of 3D-shaped Building Blocks for Use in Medicinal Chemistry and Drug Discovery

scientific article published on 01 April 2020

The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning

scholarly article published 2 August 2018

The adrenaline test for enzymes

scientific article

The enumeration of chemical space

scientific article published on 18 April 2012

The name tells the story: Two-pore channels

scientific article published on 11 May 2020

The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data

scientific article

Transfecting tissue models with CRISPR/Cas9 plasmid DNA using peptide dendrimers

scientific article published on 08 September 2020

Transfer learning enables the molecular transformer to predict regio- and stereoselective reactions on carbohydrates

scientific article published on 25 September 2020

Trypanosoma brucei Bloodstream Forms Depend upon Uptake of myo-Inositol for Golgi Complex Phosphatidylinositol Synthesis and Normal Cell Growth

scientific article published on 17 April 2015

Unexpected reactivity and mechanism of carboxamide activation in bacterial N-linked protein glycosylation

scientific article published in January 2013

Unsupervised Attention-Guided Atom-Mapping

scientific article

Unsupervised Attention-Guided Atom-Mapping

Virtual Exploration of the Ring Systems Chemical Universe

scientific article

Virtual Exploration of the Small-Molecule Chemical Universe below 160 Daltons

scientific article published on 25 February 2005

Virtual exploration of the small-molecule chemical universe below 160 Daltons

scientific article published on 01 February 2005

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening

scientific article published on 27 May 2011

Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem

scientific article

Visualization and virtual screening of the chemical universe database GDB-17.

scientific article

Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

preprint

Visualization of very large high-dimensional data sets as minimum spanning trees

article by Daniel Probst & Jean-Louis Reymond published 12 February 2020 in Journal of Cheminformatics

Web-Based Tools for Polypharmacology Prediction

scientific article published on 01 January 2019

Web-based 3D-visualization of the DrugBank chemical space

scientific article (publication date: 2016)

WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces

scientific article

What we have learned from crystal structures of proteins to receptor function ⬇️

scientific article published on July 20, 2011

X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes

scientific article published on 11 March 2019

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair

scientific article

Zinc-proline catalyzed pathway for the formation of sugars

scientific article

pH-tuned metal coordination and peroxidase activity of a peptide dendrimer enzyme model with a Fe(II)bipyridine at its core

scientific article published on 22 November 2012

α-Helix Stabilization within a Peptide Dendrimer

scientific article published on 01 December 2008

‘Ring Breaker’: Neural Network Driven Synthesis Prediction of the Ring System Chemical Space

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