The Chemical Space Project

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

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Extended-Connectivity Fingerprints

Rogers, D. O. W., & Hahn, M. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100050t · Cited by 7,597 · see citing works

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

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Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success

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ChEMBL: a large-scale bioactivity database for drug discovery

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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening

Irwin, J. J., & Shoichet, B. K. (2005) · Journal of Chemical Information and Modeling · doi:10.1021/ci049714+ · Cited by 4,058 · see citing works

ZINC: A Free Tool to Discover Chemistry for Biology

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The Properties of Known Drugs. 1. Molecular Frameworks

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Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

Rupp, M., Tkatchenko, A., Müller, K.-R., & von Lilienfeld, O. A. (2012) · Physical Review Letters · doi:10.1103/physrevlett.108.058301 · Cited by 2,312 · see citing works

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl999 · Cited by 2,145 · see citing works

Quantum chemistry structures and properties of 134 kilo molecules

Ramakrishnan, R., Dral, P. O., Rupp, M., & von Lilienfeld, O. A. (2014) · Scientific Data · doi:10.1038/sdata.2014.22 · Cited by 1,966 · see citing works

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1126 · Cited by 1,832 · see citing works

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

Ruddigkeit, L., van Deursen, R., Blum, L. C., & Reymond, J.-L. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300415d · Cited by 1,505 · see citing works

PubChem: a public information system for analyzing bioactivities of small molecules

Wang, Y., Xiao, J., Önal-Süzek, T., Zhang, J., Wang, J., & Bryant, S. H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp456 · Cited by 1,465 · see citing works

A ‘Rule of Three’ for fragment-based lead discovery?

Congreve, M., Carr, R. A. E., Murray, C. W., & Jhoti, H. (2003) · Drug Discovery Today · doi:10.1016/s1359-6446(03)02831-9 · Cited by 1,365 · see citing works

Benchmarking sets for molecular docking.

Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0608356 · Cited by 1,318 · see citing works

PubChem: Integrated Platform of Small Molecules and Biological Activities

Bolton, E., Wang, Y., Thiessen, P. A., & Bryant, S. H. (2008) · Annual reports in computational chemistry · doi:10.1016/s1574-1400(08)00012-1 · Cited by 1,267 · see citing works

Computer-based de novo design of drug-like molecules

Schneider, G., & Fechner, U. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1799 · Cited by 956 · see citing works

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

Blum, L. C., & Reymond, J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja902302h · Cited by 874 · see citing works

Similarity-based virtual screening using 2D fingerprints

Willett, P. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.10.005 · Cited by 849 · see citing works

“Scaffold-Hopping” by Topological Pharmacophore Search: A Contribution to Virtual Screening

Schneider, G., Neidhart, W. L., Giller, T., & Schmid, G. (1999) · Angewandte Chemie International Edition · doi:10.1002/(sici)1521-3773(19991004)38:19 · Cited by 715 · see citing works

RECAPRetrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry

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Novel trends in high-throughput screening

Mayr, L. M., & Bojanic, D. (2009) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2009.08.004 · Cited by 690 · see citing works

Machine learning of molecular electronic properties in chemical compound space

Montavon, G., Rupp, M., Gobre, V., Vazquez-Mayagoitia, A., Hansen, K., Tkatchenko, A., Müller, K.-R., & von Lilienfeld, O. A. (2013) · New Journal of Physics · doi:10.1088/1367-2630/15/9/095003 · Cited by 631 · see citing works

Molecular Shape Diversity of Combinatorial Libraries: A Prerequisite for Broad Bioactivity

Sauer, W., & Schwarz, M. K. (2003) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci025599w · Cited by 500 · see citing works

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

Fink, T., & Reymond, J. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci600423u · Cited by 457 · see citing works

From atoms and bonds to three-dimensional atomic coordinates: automatic model builders

Sadowski, J., & Gasteiger, J. (1993) · Chemical Reviews · doi:10.1021/cr00023a012 · Cited by 414 · see citing works

Machine learning of molecular electronic properties in chemical compound space

Montavon, G., Rupp, M., Gobre, V. V., Vázquez‐Mayagoitia, Á., Hansen, K., Tkatchenko, A., Müller, K., & von Lilienfeld, O. A. (2013) · MPG.PuRe (Max Planck Society) · doi:10.3929/ethz-b-000071765 · Cited by 414 · see citing works

Annual Reports in Computational Chemistry

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

Fink, T., Bruggesser, H., & Reymond, J. (2005) · Angewandte Chemie International Edition · doi:10.1002/anie.200462457 · Cited by 356 · see citing works

Chemography: The Art of Navigating in Chemical Space

Oprea, T. I., & Gottfries, J. (2001) · Journal of Combinatorial Chemistry · doi:10.1021/cc0000388 · Cited by 351 · see citing works

Chemical space as a source for new drugs

Reymond, J., van Deursen, R., Blum, L. C., & Ruddigkeit, L. (2010) · MedChemComm · doi:10.1039/c0md00020e · Cited by 344 · see citing works

Chemical space

Kirkpatrick, P. N., & Ellis, C. (2004) · Nature · doi:10.1038/432823a · Cited by 340 · see citing works

Heteroaromatic Rings of the Future

Pitt, W. R., Parry, D. M., Perry, B., & Groom, C. R. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm801513z · Cited by 333 · see citing works

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation

Geppert, H., Vogt, M., & Bajorath, J. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci900419k · Cited by 328 · see citing works

Exploring Chemical Space for Drug Discovery Using the Chemical Universe Database

Reymond, J., & Awale, M. (2012) · ACS Chemical Neuroscience · doi:10.1021/cn3000422 · Cited by 321 · see citing works

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

Virshup, A. M., Contreras-García, J., Wipf, P., Yang, W., & Beratan, D. N. (2013) · Journal of the American Chemical Society · doi:10.1021/ja401184g · Cited by 294 · see citing works

Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups

Ertl, P. (2002) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0255782 · Cited by 294 · see citing works

Novel Chemical Space Exploration via Natural Products

Rosén, J., Gottfries, J., Mureşan, S., Backlund, A., & Oprea, T. I. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm801514w · Cited by 284 · see citing works

Properties of Known Drugs. 2. Side Chains

Bemis, G. W., & Murcko, M. A. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm9903996 · Cited by 280 · see citing works

BitterDB: a database of bitter compounds

Dagan‐Wiener, A., Shudler, M., Levit, A., & Niv, M. Y. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr755 · Cited by 264 · see citing works

Quest for the Rings. In Silico Exploration of Ring Universe To Identify Novel Bioactive Heteroaromatic Scaffolds

Ertl, P., Jelfs, S. P., Mühlbacher, J., Schuffenhauer, A., & Selzer, P. M. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060217p · Cited by 252 · see citing works

BindingDB: A Web-Accessible Molecular Recognition Database

Chen, X., Liu, M., & Gilson, M. K. (2001) · Combinatorial Chemistry & High Throughput Screening · doi:10.2174/1386207013330670 · Cited by 224 · see citing works

Discovery and Structure−Activity Relationship of Quinuclidine Benzamides as Agonists of α7 Nicotinic Acetylcholine Receptors

Bodnar, A. L., Cortes-Burgos, L. A., Cook, K. K., Dinh, D. M., Groppi, V. E., Hajós, M., Higdon, N. R., Hoffmann, W. E., Hurst, R. S., Myers, J. K., et al. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm049363q · Cited by 216 · see citing works

A Graph-Based Genetic Algorithm and Its Application to the Multiobjective Evolution of Median Molecules

Brown, N., McKay, B., Gilardoni, F., & Gasteiger, J. (2004) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci034290p · Cited by 195 · see citing works

SPROUT: Recent developments in the de novo design of molecules

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Novel software tools for chemical diversity

Pearlman, R. S., & Smith, K. M. (1998) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1027232610247 · Cited by 176 · see citing works

Applications of artificial intelligence for chemical inference. I. Number of possible organic compounds. Acyclic structures containing carbon, hydrogen, oxygen, and nitrogen

Lederberg, J., Sutherland, G. L., Buchanan, B. G., Feigenbaum, E. A., ROBERTSON, A. V., Duffield, A. M., & Djerassi, C. (1969) · Journal of the American Chemical Society · doi:10.1021/ja01039a025 · Cited by 169 · see citing works

Visualization of the Chemical Space in Drug Discovery

Medina‐Franco, J. L., Martínez‐Mayorga, K., Giulianotti, M. A., Houghten, R. A., & Pinilla, C. (2008) · Current Computer - Aided Drug Design · doi:10.2174/157340908786786010 · Cited by 159 · see citing works

Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs

Medina‐Franco, J. L., Martínez‐Mayorga, K., Bender, A., Marín, R. M., Giulianotti, M. A., Pinilla, C., & Houghten, R. A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800379q · Cited by 152 · see citing works

Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository

Singh, N. P., Guha, R., Giulianotti, M. A., Pinilla, C., Houghten, R. A., & Medina‐Franco, J. L. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800426u · Cited by 152 · see citing works

The enumeration of chemical space

Reymond, J., Ruddigkeit, L., Blum, L. C., & van Deursen, R. (2012) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1104 · Cited by 145 · see citing works

SuperScent--a database of flavors and scents

Dunkel, M., Schmidt, U. G., Struck, S., Berger, L., Grüning, B. A., Hossbach, J., Jaeger, I. S., Effmert, U., Piechulla, B., Eriksson, R., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn695 · Cited by 144 · see citing works

Incorporation of Magnetic Nanoparticles in New Hybrid Networks Based on Heteropolyanions and Polyacrylamide

Mayer, C. R., Cabuil, V., Lalot, T., & Thouvenot, R. (1999) · Angewandte Chemie International Edition · doi:10.1002/(sici)1521-3773(19991216)38:24 · Cited by 139 · see citing works

Classification of Organic Molecules by Molecular Quantum Numbers

Nguyen, K. T., Blum, L. C., van Deursen, R., & Reymond, J. (2009) · ChemMedChem · doi:10.1002/cmdc.200900317 · Cited by 116 · see citing works

Visualization and Virtual Screening of the Chemical Universe Database GDB-17

Ruddigkeit, L., Blum, L. C., & Reymond, J. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300535x · Cited by 113 · see citing works

Molecular substructure similarity searching: efficient retrieval in two-dimensional structure databases

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The in silico world of virtual libraries

Leach, A. R. (2000) · Drug Discovery Today · doi:10.1016/s1359-6446(00)01516-6 · Cited by 107 · see citing works

Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces

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Chemoinformatics: Past, Present, and Future†

Chen, W. L. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci060016u · Cited by 105 · see citing works

SuperSweet--a resource on natural and artificial sweetening agents

Ahmed, J., Preißner, S., Dunkel, M., Worth, C. L., Eckert, A. P., & Preißner, R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq917 · Cited by 100 · see citing works

Applications of artificial intelligence for chemical inference. 22. Automatic rule formation in mass spectrometry by means of the meta-DENDRAL program

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Recent developments in automated structure elucidation of natural products

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The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules

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Flavornet: A database of aroma compounds based on odor potency in natural products

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Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17

Awale, M., & Reymond, J. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500232g · Cited by 94 · see citing works

Cheminformatics approaches to analyze diversity in compound screening libraries

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Knowledge-Based Approach to <i>de Novo</i> Design Using Reaction Vectors

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THE NUMBER OF ISOMERIC HYDROCARBONS OF THE METHANE SERIES

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Ueber die analytischen Figuren, welche in der Mathematik Bäume genannt werden und ihre Anwendung auf die Theorie chemischer Verbindungen

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MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13

Awale, M., van Deursen, R., & Reymond, J. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci300513m · Cited by 77 · see citing works

Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream

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SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules

Schwartz, J., Awale, M., & Reymond, J. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400206h · Cited by 71 · see citing works

Chemical Space Travel

van Deursen, R., & Reymond, J. (2007) · ChemMedChem · doi:10.1002/cmdc.200700021 · Cited by 69 · see citing works

Principles of the Generation of Constitutional and Configurational Isomers

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Recent Trends and Observations in the Design of High-Quality Screening Collections

Renner, S., Popov, M., Schuffenhauer, A., ROTH, H. ‐., Breitenstein, W., Marzinzik, A. L., Lewis, I., Krastel, P., Nigsch, F., Jenkins, J. L., et al. (2011) · Future Medicinal Chemistry · doi:10.4155/fmc.11.15 · Cited by 60 · see citing works

A Searchable Map of PubChem

van Deursen, R., Blum, L. C., & Reymond, J. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100237q · Cited by 60 · see citing works

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

Blum, L. C., van Deursen, R., & Reymond, J. (2011) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-011-9436-y · Cited by 59 · see citing works

Comparison of Nonbinary Similarity Coefficients for Similarity Searching, Clustering and Compound Selection

Khalifa, A. A., Harańczyk, M., & Holliday, J. D. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci8004644 · Cited by 48 · see citing works

Identification of Selective Norbornane-Type Aspartate Analogue Inhibitors of the Glutamate Transporter 1 (GLT-1) from the Chemical Universe Generated Database (GDB)

Luethi, E., Nguyen, K. T., Bürzle, M., Blum, L. C., Suzuki, Y., Hediger, M. A., & Reymond, J. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100959g · Cited by 45 · see citing works

Expanding the fragrance chemical space for virtual screening

Ruddigkeit, L., Awale, M., & Reymond, J. (2014) · Journal of Cheminformatics · doi:10.1186/1758-2946-6-27 · Cited by 45 · see citing works

Discovery of NMDA Glycine Site Inhibitors from the Chemical Universe Database GDB

Nguyen, K. T., Syed, S., Urwyler, S., Bertrand, S., Bertrand, D., & Reymond, J. (2008) · ChemMedChem · doi:10.1002/cmdc.200800198 · Cited by 41 · see citing works

Synthesis and Nicotinic Receptor Activity of Chemical Space Analogues ofN-(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)

Bréthous, L., Garcı́a-Delgado, N., Schwartz, J., Bertrand, S., Bertrand, D., & Reymond, J. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300030r · Cited by 40 · see citing works

The de novo design of median molecules within a property range of interest

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A multi-fingerprint browser for the ZINC database

Awale, M., & Reymond, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku379 · Cited by 37 · see citing works

LEAP into the Pfizer Global Virtual Library (PGVL) Space: Creation of Readily Synthesizable Design Ideas Automatically

Hu, Q., Peng, Z., Kostrowicki, J., & Kuki, A. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-931-4_13 · Cited by 36 · see citing works

Exploring the Chemical Space of Known and Unknown Organic Small Molecules at www.gdb.unibe.ch

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Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13

Blum, L. C., van Deursen, R., Bertrand, S., Mayer, M., Burgi, J. J., Bertrand, D., & Reymond, J. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200410u · Cited by 33 · see citing works

The polyhex/polypent topological paradigm: regularities in the isomer numbers and topological properties of select subclasses of benzenoid hydrocarbons and related systems

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

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

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A Survey and New Results on Computer Enumeration of Polyhex and Fusene Hydrocarbons

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

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Discovery of Potent Positive Allosteric Modulators of the α3β2 Nicotinic Acetylcholine Receptor by a Chemical Space Walk in ChEMBL

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Computer-assisted structure elucidation. Part II: Indirect database approaches and established systems

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Cluster analysis of the DrugBank chemical space using molecular quantum numbers

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Zur Statistik chemischer Verbindungen

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The art and practice of structure-based drug design: A molecular modeling perspective

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Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

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SchNet – A deep learning architecture for molecules and materials

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