Polypharmacology Browser PPB3: A Web-Based Deep Learning Tool for Target Prediction Using ChEMBL Data.

Jean-Louis Reymond University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Switzerland https://orcid.org/0000-0003-2724-2942 https://www.wikidata.org/entity/Q42719788 https://d-nb.info/gnd/130585467

Maedeh Darsaraee Sacha Javor Jean-Louis Reymond Polypharmacology Browser PPB3: A Web-Based Deep Learning Tool for Target Prediction Using ChEMBL Data. 2026 2466-2473 66 J. Chem. Inf. Model. 5 https://doi.org/10.1021/acs.jcim.6c00299 db/journals/jcisd/jcisd66.html#DarsaraeeJR26 streams/journals/jcisd

Jean-Louis Reymond Chemical space as a unifying theme for chemistry. 6 2025 December 17 J. Cheminformatics 1 https://doi.org/10.1186/s13321-025-00954-0 https://www.wikidata.org/entity/Q136309390 db/journals/jcheminf/jcheminf17.html#Reymond25 streams/journals/jcheminf

Ye Buehler Jean-Louis Reymond A View on Molecular Complexity from the GDB Chemical Space. 8405-8410 2025 65 J. Chem. Inf. Model. 16 https://doi.org/10.1021/acs.jcim.5c00334 https://www.wikidata.org/entity/Q136309400 db/journals/jcisd/jcisd65.html#BuehlerR25 streams/journals/jcisd

Francesco Leonardi Markus Orsi Jean-Louis Reymond Kaspar Riesen GEDAN: Learning the Edit Costs for Graph Edit Distance. 2025 August abs/2508.03111 CoRR https://doi.org/10.48550/arXiv.2508.03111 db/journals/corr/corr2508.html#abs-2508-03111 streams/journals/corr

Markus Orsi Jean-Louis Reymond One chiral fingerprint to find them all. 53 2024 December 16 J. Cheminformatics 1 https://doi.org/10.1186/s13321-024-00849-6 db/journals/jcheminf/jcheminf16.html#OrsiR24

Ye Buehler Jean-Louis Reymond Molecular Framework Analysis of the Generated Database GDB-13s. 484-492 2023 January 63 J. Chem. Inf. Model. 2 https://doi.org/10.1021/acs.jcim.2c01107 db/journals/jcisd/jcisd63.html#BuehlerR23

Ye Buehler Jean-Louis Reymond Expanding Bioactive Fragment Space with the Generated Database GDB-13s. 6239-6248 2023 October 63 J. Chem. Inf. Model. 20 https://doi.org/10.1021/acs.jcim.3c01096 db/journals/jcisd/jcisd63.html#BuehlerR23a

Alice Capecchi Jean-Louis Reymond Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning. 82 2021 13 J. Cheminformatics 1 https://doi.org/10.1186/s13321-021-00559-3 https://www.wikidata.org/entity/Q115715387 db/journals/jcheminf/jcheminf13.html#CapecchiR21

Philippe Schwaller Alain C. Vaucher Teodoro Laino Jean-Louis Reymond Prediction of chemical reaction yields using deep learning. 15016 2021 2 Mach. Learn. Sci. Technol. 1 https://doi.org/10.1088/2632-2153/abc81d https://www.wikidata.org/entity/Q108812232 db/journals/mlst/mlst2.html#SchwallerVLR21

Philippe Schwaller Daniel Probst Alain C. Vaucher Vishnu H. Nair David Kreutter Teodoro Laino Jean-Louis Reymond Mapping the space of chemical reactions using attention-based neural networks. 144-152 2021 3 Nat. Mach. Intell. 2 https://doi.org/10.1038/s42256-020-00284-w https://www.wikidata.org/entity/Q108812241 db/journals/natmi/natmi3.html#SchwallerPVNKLR21

Daniel Probst Jean-Louis Reymond Visualization of very large high-dimensional data sets as minimum spanning trees. 12 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-0416-x https://www.wikidata.org/entity/Q106856815 db/journals/jcheminf/jcheminf12.html#ProbstR20

Josep Arús-Pous Atanas Patronov Esben Jannik Bjerrum Christian Tyrchan Jean-Louis Reymond Hongming Chen 0001 Ola Engkvist SMILES-based deep generative scaffold decorator for de-novo drug design. 38 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-00441-8 https://www.wikidata.org/entity/Q122963839 db/journals/jcheminf/jcheminf12.html#Arus-PousPBTRCE20

Alice Capecchi Daniel Probst Jean-Louis Reymond One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. 43 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-00445-4 https://www.wikidata.org/entity/Q106856841 db/journals/jcheminf/jcheminf12.html#CapecchiPR20

Samuel Genheden Amol Thakkar Veronika Chadimová Jean-Louis Reymond Ola Engkvist Esben Jannik Bjerrum AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. 70 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-00472-1 https://www.wikidata.org/entity/Q104132867 db/journals/jcheminf/jcheminf12.html#GenhedenTCREB20

Alice Capecchi Alain Zhang Jean-Louis Reymond Populating Chemical Space with Peptides Using a Genetic Algorithm. 121-132 2020 60 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.9b01014 https://www.wikidata.org/entity/Q92199362 db/journals/jcisd/jcisd60.html#CapecchiZR20

Philippe Schwaller Daniel Probst Alain C. Vaucher Vishnu H. Nair David Kreutter Teodoro Laino Jean-Louis Reymond Mapping the Space of Chemical Reactions Using Attention-Based Neural Networks. 2020 abs/2012.06051 CoRR https://arxiv.org/abs/2012.06051 db/journals/corr/corr2012.html#abs-2012-06051

Josep Arús-Pous Thomas Blaschke Silas Ulander Jean-Louis Reymond Hongming Chen 0001 Ola Engkvist Exploring the GDB-13 chemical space using deep generative models. 20:1-20:14 2019 11 J. Cheminformatics 1 https://doi.org/10.1186/s13321-019-0341-z https://www.wikidata.org/entity/Q64103575 db/journals/jcheminf/jcheminf11.html#Arus-PousBURCE19

Josep Arús-Pous Simon Johansson Oleksii Prykhodko Esben Jannik Bjerrum Christian Tyrchan Jean-Louis Reymond Hongming Chen 0001 Ola Engkvist Randomized SMILES strings improve the quality of molecular generative models. 71:1-71:13 2019 11 J. Cheminformatics 1 https://doi.org/10.1186/s13321-019-0393-0 https://www.wikidata.org/entity/Q94204628 db/journals/jcheminf/jcheminf11.html#Arus-PousJPBTRC19

Mahendra Awale Jean-Louis Reymond Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. 10-17 2019 59 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.8b00524 https://www.wikidata.org/entity/Q90590149 db/journals/jcisd/jcisd59.html#AwaleR19

Mahendra Awale Finton Sirockin Nikolaus Stiefl Jean-Louis Reymond Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks. 1347-1356 2019 59 J. Chem. Inf. Model. 4 https://doi.org/10.1021/acs.jcim.8b00902 https://www.wikidata.org/entity/Q92601556 db/journals/jcisd/jcisd59.html#AwaleSSR19

Amol Thakkar Esben Jannik Bjerrum Ola Engkvist Jean-Louis Reymond Neural Network Guided Tree-Search Policies for Synthesis Planning. 721-724 2019 ICANN (Workshop) https://doi.org/10.1007/978-3-030-30493-5_64 conf/icann/2019w db/conf/icann/icann2019w.html#ThakkarBER19 Josep Arús-Pous Simon Johansson Oleksii Prykhodko Esben Jannik Bjerrum Christian Tyrchan Jean-Louis Reymond Hongming Chen 0001 Ola Engkvist Improving Deep Generative Models with Randomized SMILES. 747-751 2019 ICANN (Workshop) https://doi.org/10.1007/978-3-030-30493-5_68 conf/icann/2019w db/conf/icann/icann2019w.html#Arus-PousJPBTRC19

Daniel Probst Jean-Louis Reymond Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees. 2019 abs/1908.10410 CoRR http://arxiv.org/abs/1908.10410 db/journals/corr/corr1908.html#abs-1908-10410

Daniel Probst Jean-Louis Reymond FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web. 1433-1435 2018 34 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btx760 https://www.wikidata.org/entity/Q47304455 db/journals/bioinformatics/bioinformatics34.html#ProbstR18

Daniel Probst Jean-Louis Reymond A probabilistic molecular fingerprint for big data settings. 66:1-66:12 2018 10 J. Cheminformatics 1 https://doi.org/10.1186/s13321-018-0321-8 https://www.wikidata.org/entity/Q90626377 db/journals/jcheminf/jcheminf10.html#ProbstR18

Daniel Probst Jean-Louis Reymond SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript. 1-7 2018 58 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.7b00425 https://www.wikidata.org/entity/Q48094213 db/journals/jcisd/jcisd58.html#ProbstR18

Daniel Probst Jean-Louis Reymond Exploring DrugBank in Virtual Reality Chemical Space. 1731-1735 2018 58 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.8b00402 https://www.wikidata.org/entity/Q90980580 db/journals/jcisd/jcisd58.html#ProbstR18a

Mahendra Awale Jean-Louis Reymond The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. 11:1-11:10 2017 9 J. Cheminformatics 1 https://doi.org/10.1186/s13321-017-0199-x https://www.wikidata.org/entity/Q31172453 db/journals/jcheminf/jcheminf9.html#AwaleR17

Mahendra Awale Daniel Probst Jean-Louis Reymond WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. 643-649 2017 57 J. Chem. Inf. Model. 4 https://doi.org/10.1021/acs.jcim.6b00690 https://www.wikidata.org/entity/Q48107835 db/journals/jcisd/jcisd57.html#AwalePR17

Ricardo Visini Mahendra Awale Jean-Louis Reymond Fragment Database FDB-17. 700-709 2017 57 J. Chem. Inf. Model. 4 https://doi.org/10.1021/acs.jcim.7b00020 https://www.wikidata.org/entity/Q47901798 db/journals/jcisd/jcisd57.html#VisiniAR17

Víctor Sebastián-Pérez Carlos Roca Mahendra Awale Jean-Louis Reymond Ana Martínez 0001 Carmen Gil Nuria E. Campillo Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits. 2143-2151 2017 September 57 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.7b00401 https://www.wikidata.org/entity/Q48231148 db/journals/jcisd/jcisd57.html#SebastianPerezRARMGC17

Ricardo Visini Josep Arús-Pous Mahendra Awale Jean-Louis Reymond Virtual Exploration of the Ring Systems Chemical Universe. 2707-2718 2017 November 57 J. Chem. Inf. Model. 11 https://doi.org/10.1021/acs.jcim.7b00457 https://www.wikidata.org/entity/Q48210818 db/journals/jcisd/jcisd57.html#VisiniAAR17

Mahendra Awale Jean-Louis Reymond Web-based 3D-visualization of the DrugBank chemical space. 25:1-25:8 2016 8 J. Cheminformatics 1 https://doi.org/10.1186/s13321-016-0138-2 https://www.wikidata.org/entity/Q27902318 db/journals/jcheminf/jcheminf8.html#AwaleR16

Xian Jin Mahendra Awale Michaël Zasso Daniel Kostro Luc Patiny Jean-Louis Reymond PDB-Explorer: a web-based interactive map of the protein data bank in shape space. 339:1-339:15 2015 16 BMC Bioinform. https://doi.org/10.1186/s12859-015-0776-9 https://www.wikidata.org/entity/Q28608526 db/journals/bmcbi/bmcbi16.html#JinAZKPR15

Mahendra Awale Xian Jin Jean-Louis Reymond Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints. 3 2015 7 J. Cheminformatics https://doi.org/10.1186/s13321-014-0051-5 https://www.wikidata.org/entity/Q27902356 db/journals/jcheminf/jcheminf7.html#AwaleJR15

Mahendra Awale Jean-Louis Reymond Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. 1509-1516 2015 55 J. Chem. Inf. Model. 8 https://doi.org/10.1021/acs.jcim.5b00182 https://www.wikidata.org/entity/Q35710445 db/journals/jcisd/jcisd55.html#AwaleR15

Lars Ruddigkeit Mahendra Awale Jean-Louis Reymond Expanding the fragrance chemical space for virtual screening. 27 2014 6 J. Cheminformatics 1 https://doi.org/10.1186/1758-2946-6-27 https://www.wikidata.org/entity/Q33682352 db/journals/jcheminf/jcheminf6.html#RuddigkeitAR14

Tina M. Kouri Mahendra Awale James K. Slyby Jean-Louis Reymond Dinesh P. Mehta "Social" Network of Isomers Based on Bond Count Distance: Algorithms. 57-68 2014 54 J. Chem. Inf. Model. 1 https://doi.org/10.1021/ci4005173 https://www.wikidata.org/entity/Q50867911 db/journals/jcisd/jcisd54.html#KouriASRM14

Mahendra Awale Jean-Louis Reymond Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17. 1892-1907 2014 54 J. Chem. Inf. Model. 7 https://doi.org/10.1021/ci500232g https://www.wikidata.org/entity/Q43941512 db/journals/jcisd/jcisd54.html#AwaleR14

Mahendra Awale Jean-Louis Reymond A multi-fingerprint browser for the ZINC database. 234-239 2014 42 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gku379 https://www.wikidata.org/entity/Q33860664 db/journals/nar/nar42.html#AwaleR14

Lars Ruddigkeit Lorenz C. Blum Jean-Louis Reymond Visualization and Virtual Screening of the Chemical Universe Database GDB-17. 56-65 2013 53 J. Chem. Inf. Model. 1 https://doi.org/10.1021/ci300535x https://www.wikidata.org/entity/Q34319038 db/journals/jcisd/jcisd53.html#RuddigkeitBR13

Mahendra Awale Ruud van Deursen Jean-Louis Reymond MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13. 509-518 2013 53 J. Chem. Inf. Model. 2 https://doi.org/10.1021/ci300513m https://www.wikidata.org/entity/Q34321436 db/journals/jcisd/jcisd53.html#AwaleDR13

Julian Schwartz Mahendra Awale Jean-Louis Reymond SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules. 1979-1989 2013 53 J. Chem. Inf. Model. 8 https://doi.org/10.1021/ci400206h https://www.wikidata.org/entity/Q34812628 db/journals/jcisd/jcisd53.html#SchwartzAR13

Lars Ruddigkeit Ruud van Deursen Lorenz C. Blum Jean-Louis Reymond Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. 2864-2875 2012 52 J. Chem. Inf. Model. 11 https://doi.org/10.1021/ci300415d https://www.wikidata.org/entity/Q34307495 db/journals/jcisd/jcisd52.html#RuddigkeitDBR12

Lorenz C. Blum Ruud van Deursen Jean-Louis Reymond Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. 637-647 2011 25 J. Comput. Aided Mol. Des. 7 https://doi.org/10.1007/s10822-011-9436-y https://www.wikidata.org/entity/Q48057902 db/journals/jcamd/jcamd25.html#BlumDR11

Ruud van Deursen Lorenz C. Blum Jean-Louis Reymond Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. 649-662 2011 25 J. Comput. Aided Mol. Des. 7 https://doi.org/10.1007/s10822-011-9437-x https://www.wikidata.org/entity/Q33913583 db/journals/jcamd/jcamd25.html#DeursenBR11

Lorenz C. Blum Ruud van Deursen Sonia Bertrand Milena Mayer Justus J. Bürgi Daniel Bertrand Jean-Louis Reymond Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13. 3105-3112 2011 51 J. Chem. Inf. Model. 12 https://doi.org/10.1021/ci200410u https://www.wikidata.org/entity/Q34072990 db/journals/jcisd/jcisd51.html#BlumDBMBBR11

Ruud van Deursen Lorenz C. Blum Jean-Louis Reymond A Searchable Map of PubChem. 1924-1934 2010 50 J. Chem. Inf. Model. 11 https://doi.org/10.1021/ci100237q https://www.wikidata.org/entity/Q46267403 db/journals/jcisd/jcisd50.html#DeursenBR10

Tobias Fink Jean-Louis Reymond 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. 342-353 2007 47 J. Chem. Inf. Model. 2 https://doi.org/10.1021/ci600423u https://www.wikidata.org/entity/Q28649301 db/journals/jcisd/jcisd47.html#FinkR07

Josep Arús-Pous Mahendra Awale Daniel Bertrand Sonia Bertrand Esben Jannik Bjerrum Thomas Blaschke Lorenz C. Blum Ye Buehler Justus J. Bürgi Nuria E. Campillo Alice Capecchi Veronika Chadimová Hongming Chen 0001 Maedeh Darsaraee Ruud van Deursen Ola Engkvist Tobias Fink Samuel Genheden Carmen Gil Sacha Javor Xian Jin Simon Johansson Daniel Kostro Tina M. Kouri David Kreutter Teodoro Laino Francesco Leonardi Ana Martínez 0001 Milena Mayer Dinesh MehtaDinesh P. Mehta Vishnu H. Nair Markus Orsi Luc Patiny Atanas Patronov Daniel Probst Oleksii Prykhodko Kaspar Riesen Carlos Roca Lars Ruddigkeit Philippe Schwaller Julian Schwartz Víctor Sebastián-Pérez Finton Sirockin James K. Slyby Nikolaus Stiefl Amol Thakkar Christian Tyrchan Silas Ulander Alain C. Vaucher Ricardo Visini Michaël Zasso Alain Zhang