Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery. - Tobias Fink; Jean-Louis Reymond (J. Chem. Inf. Model., 2007)

A Searchable Map of PubChem. - Ruud van Deursen; Lorenz C. Blum; Jean-Louis Reymond (J. Chem. Inf. Model., 2010)

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. - Lorenz C. Blum; Ruud van Deursen; Jean-Louis Reymond (J. Comput. Aided Mol. Des., 2011)

Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. - Ruud van Deursen; Lorenz C. Blum; Jean-Louis Reymond (J. Comput. Aided Mol. Des., 2011)

Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13. - Lorenz C. Blum; Ruud van Deursen; Sonia Bertrand; Milena Mayer; Justus J. Bürgi; Daniel Bertrand; Jean-Louis Reymond (J. Chem. Inf. Model., 2011)

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. - Lars Ruddigkeit; Ruud van Deursen; Lorenz C. Blum; Jean-Louis Reymond (J. Chem. Inf. Model., 2012)

MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13. - Mahendra Awale; Ruud van Deursen; Jean-Louis Reymond (J. Chem. Inf. Model., 2013)

Visualization and Virtual Screening of the Chemical Universe Database GDB-17. - Lars Ruddigkeit; Lorenz C. Blum; Jean-Louis Reymond (J. Chem. Inf. Model., 2013)

SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules. - Julian Schwartz; Mahendra Awale; Jean-Louis Reymond (J. Chem. Inf. Model., 2013)

Expanding the fragrance chemical space for virtual screening. - Lars Ruddigkeit; Mahendra Awale; Jean-Louis Reymond (J. Cheminformatics, 2014)

Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17. - Mahendra Awale; Jean-Louis Reymond (J. Chem. Inf. Model., 2014)

"Social" Network of Isomers Based on Bond Count Distance: Algorithms. - Tina M. Kouri; Mahendra Awale; James K. Slyby; Jean-Louis Reymond; Dinesh P. Mehta (J. Chem. Inf. Model., 2014)

A multi-fingerprint browser for the ZINC database. - Mahendra Awale; Jean-Louis Reymond (Nucleic Acids Res., 2014)

PDB-Explorer: a web-based interactive map of the protein data bank in shape space. - Xian Jin; Mahendra Awale; Michaël Zasso; Daniel Kostro; Luc Patiny; Jean-Louis Reymond (BMC Bioinform., 2015)

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints. - Mahendra Awale; Xian Jin; Jean-Louis Reymond (J. Cheminformatics, 2015)

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. - Mahendra Awale; Jean-Louis Reymond (J. Chem. Inf. Model., 2015)

Web-based 3D-visualization of the DrugBank chemical space. - Mahendra Awale; Jean-Louis Reymond (J. Cheminformatics, 2016)

The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. - Mahendra Awale; Jean-Louis Reymond (J. Cheminformatics, 2017)

WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. - Mahendra Awale; Daniel Probst; Jean-Louis Reymond (J. Chem. Inf. Model., 2017)

Fragment Database FDB-17. - Ricardo Visini; Mahendra Awale; Jean-Louis Reymond (J. Chem. Inf. Model., 2017)

Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits. - Víctor Sebastián-Pérez; Carlos Roca; Mahendra Awale; Jean-Louis Reymond; Ana Martínez; Carmen Gil; Nuria E. Campillo (J. Chem. Inf. Model., 2017)

Virtual Exploration of the Ring Systems Chemical Universe. - Ricardo Visini; Josep Arús-Pous; Mahendra Awale; Jean-Louis Reymond (J. Chem. Inf. Model., 2017)

FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web. - Daniel Probst; Jean-Louis Reymond (Bioinform., 2018)

A probabilistic molecular fingerprint for big data settings. - Daniel Probst; Jean-Louis Reymond (J. Cheminformatics, 2018)

SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript. - Daniel Probst; Jean-Louis Reymond (J. Chem. Inf. Model., 2018)

Exploring DrugBank in Virtual Reality Chemical Space. - Daniel Probst; Jean-Louis Reymond (J. Chem. Inf. Model., 2018)

Improving Deep Generative Models with Randomized SMILES. - Josep Arús-Pous; Simon Johansson; Oleksii Prykhodko; Esben Jannik Bjerrum; Christian Tyrchan; Jean-Louis Reymond; Hongming Chen 001; Ola Engkvist (ICANN (Workshop), 2019)

Neural Network Guided Tree-Search Policies for Synthesis Planning. - Amol Thakkar; Esben Jannik Bjerrum; Ola Engkvist; Jean-Louis Reymond (ICANN (Workshop), 2019)

Exploring the GDB-13 chemical space using deep generative models. - Josep Arús-Pous; Thomas Blaschke; Silas Ulander; Jean-Louis Reymond; Hongming Chen 001; Ola Engkvist (J. Cheminformatics, 2019)

Randomized SMILES strings improve the quality of molecular generative models. - Josep Arús-Pous; Simon Johansson; Oleksii Prykhodko; Esben Jannik Bjerrum; Christian Tyrchan; Jean-Louis Reymond; Hongming Chen 001; Ola Engkvist (J. Cheminformatics, 2019)

Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. - Mahendra Awale; Jean-Louis Reymond (J. Chem. Inf. Model., 2019)

Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks. - Mahendra Awale; Finton Sirockin; Nikolaus Stiefl; Jean-Louis Reymond (J. Chem. Inf. Model., 2019)

SMILES-based deep generative scaffold decorator for de-novo drug design. - Josep Arús-Pous; Atanas Patronov; Esben Jannik Bjerrum; Christian Tyrchan; Jean-Louis Reymond; Hongming Chen 001; Ola Engkvist (J. Cheminformatics, 2020)

One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. - Alice Capecchi; Daniel Probst; Jean-Louis Reymond (J. Cheminformatics, 2020)

AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. - Samuel Genheden; Amol Thakkar; Veronika Chadimová; Jean-Louis Reymond; Ola Engkvist; Esben Jannik Bjerrum (J. Cheminformatics, 2020)

Visualization of very large high-dimensional data sets as minimum spanning trees. - Daniel Probst; Jean-Louis Reymond (J. Cheminformatics, 2020)

Populating Chemical Space with Peptides Using a Genetic Algorithm. - Alice Capecchi; Alain Zhang; Jean-Louis Reymond (J. Chem. Inf. Model., 2020)

Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning. - Alice Capecchi; Jean-Louis Reymond (J. Cheminformatics, 2021)

Prediction of chemical reaction yields using deep learning. - Philippe Schwaller; Alain C. Vaucher; Teodoro Laino; Jean-Louis Reymond (Mach. Learn. Sci. Technol., 2021)

Mapping the space of chemical reactions using attention-based neural networks. - Philippe Schwaller; Daniel Probst; Alain C. Vaucher; Vishnu H. Nair; David Kreutter; Teodoro Laino; Jean-Louis Reymond (Nat. Mach. Intell., 2021)

Molecular Framework Analysis of the Generated Database GDB-13s. - Ye Buehler; Jean-Louis Reymond (J. Chem. Inf. Model., 2023)

Expanding Bioactive Fragment Space with the Generated Database GDB-13s. - Ye Buehler; Jean-Louis Reymond (J. Chem. Inf. Model., 2023)

One chiral fingerprint to find them all. - Markus Orsi; Jean-Louis Reymond (J. Cheminformatics, 2024)

A View on Molecular Complexity from the GDB Chemical Space. - Ye Buehler; Jean-Louis Reymond (J. Chem. Inf. Model., 2025)

GEDAN: Learning the Edit Costs for Graph Edit Distance. - Francesco Leonardi; Markus Orsi; Jean-Louis Reymond; Kaspar Riesen (CoRR, 2025)

Chemical space as a unifying theme for chemistry. - Jean-Louis Reymond (J. Cheminformatics, 2025)