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Zhu, Di; Johannsen, Sandra; Masini, Tiziana; Simonin, Céline; Haupenthal, Jörg; Illarionov, Boris; Andreas, Anastasia; Awale, Mahendra; Gierse, Robin M; van der Laan, Tridia; van der Vlag, Ramon; Nasti, Rita; Poizat, Mael; Buhler, Eric; Reiling, Norbert; Müller, Rolf; Fischer, Markus; Reymond, Jean-Louis; Hirsch, Anna K H (2022). Discovery of novel drug-like antitubercular hits targeting the MEP pathway enzyme DXPS by strategic application of ligand-based virtual screening. Chemical Science, 13(36), pp. 10686-10698. The Royal Society of Chemistry 10.1039/d2sc02371g
Pujol-Giménez, Jonai; Poirier, Marion; Bühlmann, Sven; Schuppisser, Céline; Bhardwaj, Rajesh; Awale, Mahendra; Visini, Ricardo; Javor, Sacha; Hediger, Matthias; Reymond, Jean-Louis (2021). Inhibitors of Human Divalent Metal Transporters DMT1 (SLC11A2) and ZIP8 (SLC39A8) from a GDB-17 Fragment Library. ChemMedChem, 16(21), pp. 3306-3314. Wiley-VCH 10.1002/cmdc.202100467
Arús-Pous, Josep; Awale, Mahendra; Probst, Daniel; Reymond, Jean-Louis (2019). Exploring Chemical Space with Machine Learning. CHIMIA, 73(12), pp. 1018-1023. Schweizerische Chemische Gesellschaft 10.2533/chimia.2019.1018
Delalande, Clémence; Awale, Mahendra; Rubin, Matthias; Probst, Daniel; Ozhathil, Lijo C.; Gertsch, Jürg; Abriel, Hugues; Reymond, Jean-Louis (2019). Optimizing TRPM4 inhibitors in the MHFP6 chemical space. European journal of medicinal chemistry, 166, pp. 167-177. Elsevier 10.1016/j.ejmech.2019.01.048
Awale, Mahendra; Reymond, Jean-Louis (2019). The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. Journal of chemical information and modeling, 59(1), pp. 10-17. American Chemical Society 10.1021/acs.jcim.8b00524
Capecchi, Alice; Awale, Mahendra; Probst, Daniel; Reymond, Jean-Louis (2019). PubChem and ChEMBL beyond Lipinski. Molecular informatics, 38(5), p. 1900016. Wiley 10.1002/minf.201900016
Morstein, Johannes; Awale, Mahendra; Reymond, Jean-Louis; Trauner, Dirk (2019). Mapping the Azolog Space Enables the Optical Control of New Biological Targets. ACS central science, 5(4), pp. 607-618. ACS Publications 10.1021/acscentsci.8b00881
Awale, Mahendra; Sirockin, Finton; Stiefl, Nikolaus; Reymond, Jean-Louis (2019). Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks. Journal of chemical information and modeling, 59(4), pp. 1347-1356. American Chemical Society 10.1021/acs.jcim.8b00902
Awale, Mahendra; Sirockin, Finton; Stiefl, Nikolaus; Reymond, Jean-Louis (2019). Medicinal Chemistry Aware Database GDBMedChem. Molecular informatics, 38(8-9), p. 1900031. Wiley 10.1002/minf.201900031
Poirier, Marion; Awale, Mahendra; Rölli, Matthias A.; Giuffredi, Guy T.; Ruddigkeit, Lars; Evensen, Lasse; Stooss, Amandine; Calarco, Serafina; Lorens, James B.; Charles, Roch-Philippe; Reymond, Jean-Louis (2018). Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT-β) as the Target of a Nanomolar Angiogenesis Inhibitor from a Phenotypic Screen Using the Polypharmacology Browser PPB2. ChemMedChem, 14(2), pp. 224-236. Wiley-VCH 10.1002/cmdc.201800554
Awale, Mahendra; Reymond, Jean-Louis (2017). The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. Journal of cheminformatics, 9(11), p. 11. BioMed Central 10.1186/s13321-017-0199-x
Awale, Mahendra; Probst, Daniel; Reymond, Jean-Louis (2017). WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. Journal of chemical information and modeling, 57(4), pp. 643-649. American Chemical Society 10.1021/acs.jcim.6b00690
Visini, Ricardo; Awale, Mahendra; Reymond, Jean-Louis (2017). Fragment Database FDB-17. Journal of chemical information and modeling, 57(4), pp. 700-709. American Chemical Society 10.1021/acs.jcim.7b00020
Sebastián-Pérez, Víctor; Roca, Carlos; Awale, Mahendra; Reymond, Jean-Louis; Martinez, Ana; Gil, Carmen; Campillo, Nuria E. (2017). Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits. Journal of chemical information and modeling, 57(9), pp. 2143-2151. American Chemical Society 10.1021/acs.jcim.7b00401
Visini, Ricardo; Arus Pous, Josep; Awale, Mahendra; Reymond, Jean-Louis (2017). Virtual Exploration of the Ring Systems Chemical Universe. Journal of chemical information and modeling, 57(11), pp. 2707-2718. American Chemical Society 10.1021/acs.jcim.7b00457
Awale, Mahendra; Visini, Ricardo; Probst, Daniel; Arus Pous, Josep; Reymond, Jean-Louis (2017). Chemical Space: Big Data Challenge for Molecular Diversity. CHIMIA, 71(10), pp. 661-666. Schweizerische Chemische Gesellschaft 10.2533/chimia.2017.661
Kilchmann, Falco; Marcaida, Maria; Sachin, Kotak; Schick, Thomas; Boss, Silvan; Awale, Mahendra; Gönczy, Pierre; Reymond, Jean-Louis (2016). Discovery of a Selective Aurora A Kinase Inhibitor by Virtual Screening. Journal of medicinal chemistry, 59(15), pp. 7188-7211. American Chemical Society 10.1021/acs.jmedchem.6b00709
Awale, Mahendra; Reymond, Jean-Louis (2016). Web-based 3D-visualization of the DrugBank chemical space. Journal of cheminformatics, 8, p. 25. Springer 10.1186/s13321-016-0138-2
Jin, Xian; Awale, Mahendra; Zasso, Michaël; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis (2015). PDB-Explorer: a web-based interactive map of the protein data bank in shape space. BMC bioinformatics, 16(1), 16:339. BioMed Central 10.1186/s12859-015-0776-9
Simonin, Céline; Awale, Mahendra; Brand, Michael; van Deursen, Ruud; Schwartz, Julian; Fine, Michael; Kovacs, Gergely; Häfliger, Pascal; Gyimesi, Gergely; Sithampari, Abilashan; Charles, Roch-Philippe; Hediger, Matthias; Reymond, Jean-Louis (2015). Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand-Based Virtual Screening Method. Angewandte Chemie (International ed.), 54(49), pp. 14748-14752. Wiley-VCH 10.1002/anie.201507320
Awale, Mahendra; Reymond, Jean-Louis (2015). Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. Journal of chemical information and modeling, 55(8), pp. 1509-1516. American Chemical Society 10.1021/acs.jcim.5b00182
Montalbetti, Nicolas; Simonin, Alexandre; Simonin, Céline; Awale, Mahendra; Reymond, Jean-Louis; Hediger, Matthias (2015). Discovery and characterization of a novel non-competitive inhibitor of the divalent metal transporter DMT1/SLC11A2. Biochemical pharmacology, 96(3), pp. 216-224. Elsevier 10.1016/j.bcp.2015.05.002
Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis (2015). Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints. Journal of cheminformatics, 7(1), p. 3. Springer 10.1186/s13321-014-0051-5
Awale, Mahendra; Reymond, Jean-Louis (2014). Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17. Journal of chemical information and modeling, 54(7), pp. 1892-1907. American Chemical Society 10.1021/ci500232g
Ruddigkeit, Lars; Awale, Mahendra; Reymond, Jean-Louis (2014). Expanding the fragrance chemical space for virtual screening. Journal of cheminformatics, 6(1), p. 27. Springer 10.1186/1758-2946-6-27
Bürgi, Justus; Awale, Mahendra; Boss, Silvan D.; Schaer, Tifany; Marger, Fabrice; Viveros Paredes, Juan Manuel; Bertrand, Sonia; Gertsch, Jürg; Bertrand, Daniel; Reymond, Jean-Louis (2014). Discovery of Potent Positive Allosteric Modulators of the α3β2 Nicotinic Acetylcholine Receptor by a Chemical Space Walk in ChEMBL. ACS chemical neuroscience, 5(5), pp. 346-359. American Chemical Society 10.1021/cn4002297
Awale, Mahendra; Reymond, Jean-Louis (2014). A multi-fingerprint browser for the ZINC database. Nucleic acids research, 42(W1), W234-W239. Information Retrieval Ltd. 10.1093/nar/gku379
Kouri, Tina M.; Awale, Mahendra; Slyby, James K.; Reymond, Jean-Louis; Mehta, Dinesh P. (2014). “Social” Network of Isomers Based on Bond Count Distance: Algorithms. Journal of chemical information and modeling, 54(1), pp. 57-68. American Chemical Society 10.1021/ci4005173
Awale, Mahendra; van Deursen, Ruud; Reymond, Jean-Louis (2013). MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13. Journal of chemical information and modeling, 53(2), pp. 509-518. American Chemical Society 10.1021/ci300513m
Schwartz, Julian; Awale, Mahendra; Reymond, Jean-Louis (2013). SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules. Journal of chemical information and modeling, 53(8), pp. 1979-1989. American Chemical Society 10.1021/ci400206h
Awale, Mahendra; Reymond, Jean-Louis (2012). Cluster analysis of the DrugBank chemical space using molecular quantum numbers. Bioorganic & medicinal chemistry, 20(18), pp. 5372-5378. Amsterdam: Elsevier 10.1016/j.bmc.2012.03.017
Reymond, Jean-Louis; Awale, Mahendra (2012). Exploring Chemical Space for Drug Discovery Using the Chemical Universe Database. ACS chemical neuroscience, 3(9), pp. 649-657. Washington, D.C.: American Chemical Society 10.1021/cn3000422
Awale, Mahendra; Reymond, Jean-Louis (2019). Web-Based Tools for Polypharmacology Prediction. In: Ziegler, Slava; Waldmann, Herbert (eds.) Systems Chemical Biology. Methods in molecular biology: Vol. 1888 (pp. 255-272). Humana Press 10.1007/978-1-4939-8891-4_15
Reymond, Jean-Louis; Visini, Ricardo; Awale, Mahendra (2016). Enumeration of Chemical Fragment Space. In: Erlanson, Daniel A.; Jahnke, Wolfgang (eds.) Fragment-based Drug Discovery Lessons and Outlook. Methods and Principles in Medicinal Chemistry (pp. 57-74). Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA 10.1002/9783527683604.ch03
Reymond, Jean-Louis; Ruddigkeit, Lars; Awale, Mahendra (2014). Considerations on the Drug-Like Chemical Space. In: Jacoby, Edgar (ed.) Computational Chemogenomics (pp. 39-64). Singapore: Pan Stanford Publishing
Capecchi, Alice; Awale, Mahendra; Probst, Daniel; Reymond, Jean-Louis (2018). Beyond Lipinski – an analysis of the PubChem chemical space (Unpublished). In: Summer School on Machine Learning in Drug Design. Leuven, Belgium. Monday, August 20, 2018 - to Wednesday, August 22, 2018.
